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

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

      setCorrFuncType("Legendre Correlation Function of Z");
      setOutputName(getPrefix(dumpFilename_) + ".lcorrZ");
      histogram_.resize(nTimeBins_);
      counts_.resize(nTimeBins_);
      for (int i = 0; i < nTimeBins_; i++) {
        histogram_[i].resize(nZBins_);
        counts_[i].resize(nZBins_);
      }
      LegendrePolynomial polynomial(order);
      legendre_ = polynomial.getLegendrePolynomial(order);
    }

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

    Mat3x3d hmat = snapshot1->getHmat();
    RealType halfBoxZ_ = hmat(2,2) / 2.0;      

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

    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);

    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 pos = sd1->getPos();
      if (info_->getSimParams()->getUsePeriodicBoundaryConditions())
        snapshot1->wrapVector(pos);
      int zBin = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2));

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

  void LegendreCorrFuncZ::postCorrelate() {
    for (int i =0 ; i < nTimeBins_; ++i) {
      for (int j = 0; j < nZBins_; ++j) {
        if (counts_[i][j] > 0) {
          histogram_[i][j] /= counts_[i][j];
        }
      }
    }
  }

  void LegendreCorrFuncZ::preCorrelate() {
    for (int i = 0; i < nTimeBins_; i++) {
      std::fill(histogram_[i].begin(), histogram_[i].end(), Vector3d(0.0));
      std::fill(counts_[i].begin(), counts_[i].end(), 0);
    }
  }


  Vector3d LegendreCorrFuncZ::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 LegendreCorrFuncZ::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 LegendreCorrFuncZ::writeCorrelate() {
    std::ofstream ofs(getOutputFileName().c_str());

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#time\tPn(costheta_z)\n";

      for (int i = 0; i < nTimeBins_; ++i) {

        ofs << time_[i];

        for (int j = 0; j < nZBins_; ++j) {          
          ofs << "\t" << histogram_[i][j](2);
        }
        ofs << "\n";
      }
            
    } else {
      sprintf(painCave.errMsg,
              "LegendreCorrFuncZ::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();        
    }
    ofs.close();    
  }
}
Revision:	1915
Committed:	Mon Jul 29 17:55:17 2013 UTC (12 years, 4 months ago) by gezelter
File size:	6938 byte(s)
Log Message:	Added Legendre Correlation function (as a function of Z), working on architecture for Ewald Fixed some bugs in FlucQ
#	User	Rev	Content
1	gezelter	1915	/*
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, 234107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include "applications/dynamicProps/LegendreCorrFuncZ.hpp"
44			#include "math/LegendrePolynomial.hpp"
45			#include "utils/simError.h"
46
47			namespace OpenMD {
48			LegendreCorrFuncZ::LegendreCorrFuncZ(SimInfo* info,
49			const std::string& filename,
50			const std::string& sele1,
51			const std::string& sele2,
52			int order, int nZbins,
53			long long int memSize)
54			: ParticleTimeCorrFunc(info, filename, sele1, sele2,
55			DataStorage::dslAmat, memSize), nZBins_(nZbins) {
56
57			setCorrFuncType("Legendre Correlation Function of Z");
58			setOutputName(getPrefix(dumpFilename_) + ".lcorrZ");
59			histogram_.resize(nTimeBins_);
60			counts_.resize(nTimeBins_);
61			for (int i = 0; i < nTimeBins_; i++) {
62			histogram_[i].resize(nZBins_);
63			counts_[i].resize(nZBins_);
64			}
65			LegendrePolynomial polynomial(order);
66			legendre_ = polynomial.getLegendrePolynomial(order);
67			}
68
69			void LegendreCorrFuncZ::correlateFrames(int frame1, int frame2) {
70			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
71			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
72			assert(snapshot1 && snapshot2);
73
74			Mat3x3d hmat = snapshot1->getHmat();
75			RealType halfBoxZ_ = hmat(2,2) / 2.0;
76
77			RealType time1 = snapshot1->getTime();
78			RealType time2 = snapshot2->getTime();
79
80			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
81
82			int i;
83			int j;
84			StuntDouble* sd1;
85			StuntDouble* sd2;
86
87			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
88			sd1 != NULL && sd2 != NULL;
89			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
90
91			Vector3d pos = sd1->getPos();
92			if (info_->getSimParams()->getUsePeriodicBoundaryConditions())
93			snapshot1->wrapVector(pos);
94			int zBin = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2));
95
96			Vector3d corrVals = calcCorrVals(frame1, frame2, sd1, sd2);
97			histogram_[timeBin][zBin] += corrVals;
98			counts_[timeBin][zBin]++;
99			}
100
101			}
102
103			void LegendreCorrFuncZ::postCorrelate() {
104			for (int i =0 ; i < nTimeBins_; ++i) {
105			for (int j = 0; j < nZBins_; ++j) {
106			if (counts_[i][j] > 0) {
107			histogram_[i][j] /= counts_[i][j];
108			}
109			}
110			}
111			}
112
113			void LegendreCorrFuncZ::preCorrelate() {
114			for (int i = 0; i < nTimeBins_; i++) {
115			std::fill(histogram_[i].begin(), histogram_[i].end(), Vector3d(0.0));
116			std::fill(counts_[i].begin(), counts_[i].end(), 0);
117			}
118			}
119
120
121
122			Vector3d LegendreCorrFuncZ::calcCorrVals(int frame1, int frame2, StuntDouble* sd1, StuntDouble* sd2) {
123
124			// The lab frame vector corresponding to the body-fixed
125			// z-axis is simply the second column of A.transpose()
126			// or, identically, the second row of A itself.
127			// Similar identites give the 0th and 1st rows of A for
128			// the lab vectors associated with body-fixed x- and y- axes.
129
130			Vector3d v1x = sd1->getA(frame1).getRow(0);
131			Vector3d v2x = sd2->getA(frame2).getRow(0);
132			Vector3d v1y = sd1->getA(frame1).getRow(1);
133			Vector3d v2y = sd2->getA(frame2).getRow(1);
134			Vector3d v1z = sd1->getA(frame1).getRow(2);
135			Vector3d v2z = sd2->getA(frame2).getRow(2);
136
137			RealType uxprod = legendre_.evaluate(dot(v1x, v2x)/(v1x.length()*v2x.length()));
138			RealType uyprod = legendre_.evaluate(dot(v1y, v2y)/(v1y.length()*v2y.length()));
139			RealType uzprod = legendre_.evaluate(dot(v1z, v2z)/(v1z.length()*v2z.length()));
140
141			return Vector3d(uxprod, uyprod, uzprod);
142
143			}
144
145
146			void LegendreCorrFuncZ::validateSelection(const SelectionManager& seleMan) {
147			StuntDouble* sd;
148			int i;
149			for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
150			if (!sd->isDirectionalAtom()) {
151			sprintf(painCave.errMsg,
152			"LegendreCorrFunc::validateSelection Error: selected atoms are not Directional\n");
153			painCave.isFatal = 1;
154			simError();
155			}
156			}
157
158			}
159
160			void LegendreCorrFuncZ::writeCorrelate() {
161			std::ofstream ofs(getOutputFileName().c_str());
162
163			if (ofs.is_open()) {
164
165			ofs << "#" << getCorrFuncType() << "\n";
166			ofs << "#time\tPn(costheta_z)\n";
167
168			for (int i = 0; i < nTimeBins_; ++i) {
169
170			ofs << time_[i];
171
172			for (int j = 0; j < nZBins_; ++j) {
173			ofs << "\t" << histogram_[i][j](2);
174			}
175			ofs << "\n";
176			}
177
178			} else {
179			sprintf(painCave.errMsg,
180			"LegendreCorrFuncZ::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
181			painCave.isFatal = 1;
182			simError();
183			}
184			ofs.close();
185			}
186			}