applications/staticProps/TwoDGofR.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 <algorithm>
#include <fstream>
#include "applications/staticProps/TwoDGofR.hpp"
#include "utils/simError.h"

namespace OpenMD {

  TwoDGofR::TwoDGofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, RealType dz, int nrbins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){

      deltaR_ = len_ /nRBins_;

      deltaZ_ = dz;
    
      histogram_.resize(nRBins_);
      avgTwoDGofR_.resize(nRBins_);

      setOutputName(getPrefix(filename) + ".TwoDGofR");
    }


  void TwoDGofR::preProcess() {
    std::fill(avgTwoDGofR_.begin(), avgTwoDGofR_.end(), 0.0);    
  }

  void TwoDGofR::initializeHistogram() {
    std::fill(histogram_.begin(), histogram_.end(), 0);
  }


  void TwoDGofR::processHistogram() {

    int nPairs = getNPairs();

    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();

    RealType volume = hmat(0,0) * hmat(1,1) * deltaZ_;

    RealType pairDensity = nPairs /volume * 2.0;
    RealType pairConstant = (NumericConstant::PI * pairDensity);

    for(unsigned int i = 0 ; i < histogram_.size(); ++i){

      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice = deltaZ_ * (( rUpper*rUpper ) - ( rLower*rLower ));
      RealType nIdeal = volSlice * pairConstant;
      
      avgTwoDGofR_[i] += histogram_[i] / nIdeal;    
    }

  }

  void TwoDGofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {

    if (sd1 == sd2) {
      return;
    }
    
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos2 - pos1;
    if (usePeriodicBoundaryConditions_)
      currentSnapshot_->wrapVector(r12);

    RealType distance = sqrt(r12.x()*r12.x() + r12.y()*r12.y());

    if (distance < len_) {
      int whichBin = int(distance / deltaR_);
      histogram_[whichBin] += 2;
    }
  }


  void TwoDGofR::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#2D radial distribution function\n";
      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
      rdfStream << "#r\tcorrValue\n";
      for (unsigned int i = 0; i < avgTwoDGofR_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);
        rdfStream << r << "\t" << avgTwoDGofR_[i]/nProcessed_ << "\n";
      }
        
    } else {

      sprintf(painCave.errMsg, "TwoDGofR: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }

    rdfStream.close();
  }

}

Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	4816 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	gezelter	1454	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1454	*/
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/TwoDGofR.hpp"
46			#include "utils/simError.h"
47
48			namespace OpenMD {
49
50			TwoDGofR::TwoDGofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, RealType dz, int nrbins)
51			: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
52
53			deltaR_ = len_ /nRBins_;
54
55			deltaZ_ = dz;
56
57			histogram_.resize(nRBins_);
58			avgTwoDGofR_.resize(nRBins_);
59
60			setOutputName(getPrefix(filename) + ".TwoDGofR");
61			}
62
63
64			void TwoDGofR::preProcess() {
65			std::fill(avgTwoDGofR_.begin(), avgTwoDGofR_.end(), 0.0);
66			}
67
68	jmichalk	1785	void TwoDGofR::initializeHistogram() {
69	gezelter	1454	std::fill(histogram_.begin(), histogram_.end(), 0);
70			}
71
72
73			void TwoDGofR::processHistogram() {
74
75			int nPairs = getNPairs();
76
77			Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
78
79			RealType volume = hmat(0,0) * hmat(1,1) * deltaZ_;
80
81			RealType pairDensity = nPairs /volume * 2.0;
82			RealType pairConstant = (NumericConstant::PI * pairDensity);
83
84	gezelter	1782	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
85	gezelter	1454
86			RealType rLower = i * deltaR_;
87			RealType rUpper = rLower + deltaR_;
88			RealType volSlice = deltaZ_ * (( rUpperrUpper ) - ( rLowerrLower ));
89			RealType nIdeal = volSlice * pairConstant;
90
91			avgTwoDGofR_[i] += histogram_[i] / nIdeal;
92			}
93
94			}
95
96			void TwoDGofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
97
98			if (sd1 == sd2) {
99			return;
100			}
101
102			Vector3d pos1 = sd1->getPos();
103			Vector3d pos2 = sd2->getPos();
104			Vector3d r12 = pos2 - pos1;
105			if (usePeriodicBoundaryConditions_)
106			currentSnapshot_->wrapVector(r12);
107
108			RealType distance = sqrt(r12.x()r12.x() + r12.y()r12.y());
109
110			if (distance < len_) {
111	gezelter	1790	int whichBin = int(distance / deltaR_);
112	gezelter	1454	histogram_[whichBin] += 2;
113			}
114			}
115
116
117			void TwoDGofR::writeRdf() {
118			std::ofstream rdfStream(outputFilename_.c_str());
119			if (rdfStream.is_open()) {
120			rdfStream << "#2D radial distribution function\n";
121			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
122			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
123			rdfStream << "#r\tcorrValue\n";
124	gezelter	1782	for (unsigned int i = 0; i < avgTwoDGofR_.size(); ++i) {
125	gezelter	1454	RealType r = deltaR_ * (i + 0.5);
126			rdfStream << r << "\t" << avgTwoDGofR_[i]/nProcessed_ << "\n";
127			}
128
129			} else {
130
131			sprintf(painCave.errMsg, "TwoDGofR: unable to open %s\n", outputFilename_.c_str());
132			painCave.isFatal = 1;
133			simError();
134			}
135
136			rdfStream.close();
137			}
138
139			}
140