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]  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/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::initializeHistogram() {
    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(unsigned 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 (unsigned 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:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	4638 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	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	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	306	*/
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/GofR.hpp"
46	tim	307	#include "utils/simError.h"
47	tim	306
48	gezelter	1390	namespace OpenMD {
49	tim	306
50	tim	963	GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
51	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
52	tim	306
53	gezelter	507	deltaR_ = len_ /nRBins_;
54	tim	310
55	gezelter	507	histogram_.resize(nRBins_);
56			avgGofr_.resize(nRBins_);
57	tim	311
58	gezelter	507	setOutputName(getPrefix(filename) + ".gofr");
59			}
60	tim	306
61
62	gezelter	507	void GofR::preProcess() {
63	tim	306	std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);
64	gezelter	507	}
65	tim	306
66	jmichalk	1785	void GofR::initializeHistogram() {
67	tim	306	std::fill(histogram_.begin(), histogram_.end(), 0);
68	gezelter	507	}
69	tim	306
70
71	gezelter	507	void GofR::processHistogram() {
72	tim	306
73	tim	353	int nPairs = getNPairs();
74	tim	963	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
75			RealType pairDensity = nPairs /volume * 2.0;
76			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
77	tim	306
78	gezelter	1782	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
79	tim	306
80	tim	963	RealType rLower = i * deltaR_;
81			RealType rUpper = rLower + deltaR_;
82			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
83			RealType nIdeal = volSlice * pairConstant;
84	tim	306
85	gezelter	507	avgGofr_[i] += histogram_[i] / nIdeal;
86	tim	306	}
87
88	gezelter	507	}
89	tim	306
90	gezelter	507	void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
91	tim	306
92			if (sd1 == sd2) {
93	gezelter	507	return;
94	tim	306	}
95
96			Vector3d pos1 = sd1->getPos();
97			Vector3d pos2 = sd2->getPos();
98	tim	361	Vector3d r12 = pos2 - pos1;
99	gezelter	1078	if (usePeriodicBoundaryConditions_)
100			currentSnapshot_->wrapVector(r12);
101	tim	306
102	tim	963	RealType distance = r12.length();
103	tim	307
104	tim	328	if (distance < len_) {
105	gezelter	507	int whichBin = distance / deltaR_;
106			histogram_[whichBin] += 2;
107	tim	328	}
108	gezelter	507	}
109	tim	306
110
111	gezelter	507	void GofR::writeRdf() {
112	tim	306	std::ofstream rdfStream(outputFilename_.c_str());
113			if (rdfStream.is_open()) {
114	gezelter	507	rdfStream << "#radial distribution function\n";
115			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
116			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
117			rdfStream << "#r\tcorrValue\n";
118	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
119	tim	963	RealType r = deltaR_ * (i + 0.5);
120	gezelter	507	rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
121			}
122	tim	306	} 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