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:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (14 years, 1 month ago) by gezelter
File size:	6446 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	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	1596	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			}