applications/staticProps/GofXyz.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

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

namespace oopse {

GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins) {
    setOutputName(getPrefix(filename) + ".gxyz");

    deltaR_ = len_ / nRBins_;
    
    histogram_.resize(nRBins_);
    for (int i = 0 ; i < nRBins_; ++i) {
        histogram_[i].resize(nRBins_);
        for(int j = 0; j < nRBins_; ++j) {
            histogram_[i][j].resize(nRBins_);
        }
    }   
}


void GofXyz::preProcess() {
    /*
    for (int i = 0; i < avgGofr_.size(); ++i) {
        std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
    }
    */
}

void GofXyz::initalizeHistogram() {
    /*
    npairs_ = 0;
    for (int i = 0; i < histogram_.size(); ++i)
        std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
    */
}


void GofXyz::processHistogram() {

    /*
    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    double pairDensity = npairs_ /volume;
    double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;

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

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

        for (int j = 0; j < histogram_[i].size(); ++j){
            avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
        }
    }
    */
}

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

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

    double distance = r12.length();
    int whichRBin = distance / deltaR_;

    
    double cosAngle = evaluateAngle(sd1, sd2);
    double halfBin = (nAngleBins_ - 1) * 0.5;
    int whichThetaBin = halfBin * (cosAngle + 1.0)
    ++histogram_[whichRBin][whichThetaBin];
    
    ++npairs_;
    */
}

void GofXyz::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 < histogram_.size(); ++i) {
            double x = deltaR_ * (i + 0.5);

            for(int j = 0; j < histogram_[i].size(); ++j) {
                double y = deltaR_ * (j+ 0.5);

                for(int k = 0;k < histogram_[i].size(); ++k) {
                    double z = deltaR_ * (k + 0.5); 
                    rdfStream << x << "\t" << y << "\t" <<  z << "\t" << histogram_[i][j][k]/nProcessed_ << "\n";
                }
            }
        }
        
    } else {


    }

    rdfStream.close();
}

}


Revision:	2038
Committed:	Wed Feb 16 20:30:50 2005 UTC (19 years, 4 months ago) by tim
File size:	5190 byte(s)
Log Message:	change the default bin number
#	User	Rev	Content
1	tim	1994	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <algorithm>
43			#include <fstream>
44			#include "applications/staticProps/GofXyz.hpp"
45			#include "utils/simError.h"
46
47			namespace oopse {
48
49	tim	2038	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
50			: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins) {
51	tim	1995	setOutputName(getPrefix(filename) + ".gxyz");
52	tim	1994
53	tim	2038	deltaR_ = len_ / nRBins_;
54
55			histogram_.resize(nRBins_);
56			for (int i = 0 ; i < nRBins_; ++i) {
57			histogram_[i].resize(nRBins_);
58			for(int j = 0; j < nRBins_; ++j) {
59			histogram_[i][j].resize(nRBins_);
60			}
61			}
62	tim	1994	}
63
64
65			void GofXyz::preProcess() {
66	tim	1995	/*
67	tim	1994	for (int i = 0; i < avgGofr_.size(); ++i) {
68			std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
69			}
70	tim	1995	*/
71	tim	1994	}
72
73			void GofXyz::initalizeHistogram() {
74	tim	1995	/*
75	tim	1994	npairs_ = 0;
76			for (int i = 0; i < histogram_.size(); ++i)
77			std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
78	tim	1995	*/
79	tim	1994	}
80
81
82			void GofXyz::processHistogram() {
83
84	tim	1995	/*
85	tim	1994	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
86			double pairDensity = npairs_ /volume;
87	tim	1995	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
88	tim	1994
89			for(int i = 0 ; i < histogram_.size(); ++i){
90
91			double rLower = i * deltaR_;
92			double rUpper = rLower + deltaR_;
93			double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
94			double nIdeal = volSlice * pairConstant;
95
96			for (int j = 0; j < histogram_[i].size(); ++j){
97			avgGofr_[i][j] += histogram_[i][j] / nIdeal;
98			}
99			}
100	tim	1995	*/
101	tim	1994	}
102
103			void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
104
105	tim	1995	/*
106	tim	1994	if (sd1 == sd2) {
107			return;
108			}
109
110			Vector3d pos1 = sd1->getPos();
111			Vector3d pos2 = sd2->getPos();
112			Vector3d r12 = pos1 - pos2;
113			currentSnapshot_->wrapVector(r12);
114
115			double distance = r12.length();
116			int whichRBin = distance / deltaR_;
117
118
119			double cosAngle = evaluateAngle(sd1, sd2);
120			double halfBin = (nAngleBins_ - 1) * 0.5;
121			int whichThetaBin = halfBin * (cosAngle + 1.0)
122			++histogram_[whichRBin][whichThetaBin];
123
124			++npairs_;
125	tim	1995	*/
126	tim	1994	}
127
128			void GofXyz::writeRdf() {
129			std::ofstream rdfStream(outputFilename_.c_str());
130			if (rdfStream.is_open()) {
131			rdfStream << "#radial distribution function\n";
132			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
133			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
134			rdfStream << "#r\tcorrValue\n";
135			for (int i = 0; i < histogram_.size(); ++i) {
136			double x = deltaR_ * (i + 0.5);
137
138			for(int j = 0; j < histogram_[i].size(); ++j) {
139			double y = deltaR_ * (j+ 0.5);
140
141			for(int k = 0;k < histogram_[i].size(); ++k) {
142	tim	1995	double z = deltaR_ * (k + 0.5);
143			rdfStream << x << "\t" << y << "\t" << z << "\t" << histogram_[i][j][k]/nProcessed_ << "\n";
144			}
145	tim	1994	}
146			}
147
148			} else {
149
150
151			}
152
153			rdfStream.close();
154			}
155
156			}
157
158
159