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

namespace OpenMD {

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

      deltaR_ = len_ /nRBins_;
    
      histogram_.resize(nRBins_);
      avgGofr_.resize(nRBins_);

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


  void GofR::preProcess() {
    std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);    
  }

  void GofR::initalizeHistogram() {
    std::fill(histogram_.begin(), histogram_.end(), 0);
  }


  void GofR::processHistogram() {

    int nPairs = getNPairs();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs /volume * 2.0;
    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;

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

      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
      RealType nIdeal = volSlice * pairConstant;

      avgGofr_[i] += histogram_[i] / nIdeal;    
    }

  }

  void GofR::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 = r12.length();

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


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

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

    rdfStream.close();
  }

}

Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/applications/staticProps/GofR.cpp*
File size:	4562 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	tim	306	/*
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	306	* 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	306	* 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	306	*/
41
42			#include <algorithm>
43			#include <fstream>
44			#include "applications/staticProps/GofR.hpp"
45	tim	307	#include "utils/simError.h"
46	tim	306
47	gezelter	1390	namespace OpenMD {
48	tim	306
49	tim	963	GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
50	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
51	tim	306
52	gezelter	507	deltaR_ = len_ /nRBins_;
53	tim	310
54	gezelter	507	histogram_.resize(nRBins_);
55			avgGofr_.resize(nRBins_);
56	tim	311
57	gezelter	507	setOutputName(getPrefix(filename) + ".gofr");
58			}
59	tim	306
60
61	gezelter	507	void GofR::preProcess() {
62	tim	306	std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);
63	gezelter	507	}
64	tim	306
65	gezelter	507	void GofR::initalizeHistogram() {
66	tim	306	std::fill(histogram_.begin(), histogram_.end(), 0);
67	gezelter	507	}
68	tim	306
69
70	gezelter	507	void GofR::processHistogram() {
71	tim	306
72	tim	353	int nPairs = getNPairs();
73	tim	963	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
74			RealType pairDensity = nPairs /volume * 2.0;
75			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
76	tim	306
77			for(int i = 0 ; i < histogram_.size(); ++i){
78
79	tim	963	RealType rLower = i * deltaR_;
80			RealType rUpper = rLower + deltaR_;
81			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
82			RealType nIdeal = volSlice * pairConstant;
83	tim	306
84	gezelter	507	avgGofr_[i] += histogram_[i] / nIdeal;
85	tim	306	}
86
87	gezelter	507	}
88	tim	306
89	gezelter	507	void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
90	tim	306
91			if (sd1 == sd2) {
92	gezelter	507	return;
93	tim	306	}
94
95			Vector3d pos1 = sd1->getPos();
96			Vector3d pos2 = sd2->getPos();
97	tim	361	Vector3d r12 = pos2 - pos1;
98	gezelter	1078	if (usePeriodicBoundaryConditions_)
99			currentSnapshot_->wrapVector(r12);
100	tim	306
101	tim	963	RealType distance = r12.length();
102	tim	307
103	tim	328	if (distance < len_) {
104	gezelter	507	int whichBin = distance / deltaR_;
105			histogram_[whichBin] += 2;
106	tim	328	}
107	gezelter	507	}
108	tim	306
109
110	gezelter	507	void GofR::writeRdf() {
111	tim	306	std::ofstream rdfStream(outputFilename_.c_str());
112			if (rdfStream.is_open()) {
113	gezelter	507	rdfStream << "#radial distribution function\n";
114			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
115			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
116			rdfStream << "#r\tcorrValue\n";
117			for (int i = 0; i < avgGofr_.size(); ++i) {
118	tim	963	RealType r = deltaR_ * (i + 0.5);
119	gezelter	507	rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
120			}
121	tim	306
122			} else {
123
124	gezelter	507	sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str());
125			painCave.isFatal = 1;
126			simError();
127	tim	306	}
128	tim	307
129			rdfStream.close();
130	gezelter	507	}
131	tim	306
132			}
133