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)
    : RadialDistrFunc(info, filename, sele1, sele2){
    setOutputName(getPrefix(filename) + ".gxyz");

}


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:	1995
Committed:	Thu Feb 10 22:37:21 2005 UTC (19 years, 5 months ago) by tim
File size:	4882 byte(s)
Log Message:	more work in StaticProps
#	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			GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50			: RadialDistrFunc(info, filename, sele1, sele2){
51	tim	1995	setOutputName(getPrefix(filename) + ".gxyz");
52	tim	1994
53			}
54
55
56			void GofXyz::preProcess() {
57	tim	1995	/*
58	tim	1994	for (int i = 0; i < avgGofr_.size(); ++i) {
59			std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
60			}
61	tim	1995	*/
62	tim	1994	}
63
64			void GofXyz::initalizeHistogram() {
65	tim	1995	/*
66	tim	1994	npairs_ = 0;
67			for (int i = 0; i < histogram_.size(); ++i)
68			std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
69	tim	1995	*/
70	tim	1994	}
71
72
73			void GofXyz::processHistogram() {
74
75	tim	1995	/*
76	tim	1994	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
77			double pairDensity = npairs_ /volume;
78	tim	1995	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
79	tim	1994
80			for(int i = 0 ; i < histogram_.size(); ++i){
81
82			double rLower = i * deltaR_;
83			double rUpper = rLower + deltaR_;
84			double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
85			double nIdeal = volSlice * pairConstant;
86
87			for (int j = 0; j < histogram_[i].size(); ++j){
88			avgGofr_[i][j] += histogram_[i][j] / nIdeal;
89			}
90			}
91	tim	1995	*/
92	tim	1994	}
93
94			void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
95
96	tim	1995	/*
97	tim	1994	if (sd1 == sd2) {
98			return;
99			}
100
101			Vector3d pos1 = sd1->getPos();
102			Vector3d pos2 = sd2->getPos();
103			Vector3d r12 = pos1 - pos2;
104			currentSnapshot_->wrapVector(r12);
105
106			double distance = r12.length();
107			int whichRBin = distance / deltaR_;
108
109
110			double cosAngle = evaluateAngle(sd1, sd2);
111			double halfBin = (nAngleBins_ - 1) * 0.5;
112			int whichThetaBin = halfBin * (cosAngle + 1.0)
113			++histogram_[whichRBin][whichThetaBin];
114
115			++npairs_;
116	tim	1995	*/
117	tim	1994	}
118
119			void GofXyz::writeRdf() {
120			std::ofstream rdfStream(outputFilename_.c_str());
121			if (rdfStream.is_open()) {
122			rdfStream << "#radial distribution function\n";
123			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
124			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
125			rdfStream << "#r\tcorrValue\n";
126			for (int i = 0; i < histogram_.size(); ++i) {
127			double x = deltaR_ * (i + 0.5);
128
129			for(int j = 0; j < histogram_[i].size(); ++j) {
130			double y = deltaR_ * (j+ 0.5);
131
132			for(int k = 0;k < histogram_[i].size(); ++k) {
133	tim	1995	double z = deltaR_ * (k + 0.5);
134			rdfStream << x << "\t" << y << "\t" << z << "\t" << histogram_[i][j][k]/nProcessed_ << "\n";
135			}
136	tim	1994	}
137			}
138
139			} else {
140
141
142			}
143
144			rdfStream.close();
145			}
146
147			}
148
149
150