applications/staticProps/GofRAngle.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/GofRAngle.hpp"
#include "utils/simError.h"

namespace oopse {

GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, 
    const std::string& sele2, double len, int nrbins, int nangleBins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){

    deltaR_ = len_ /nRBins_;             
    deltaCosAngle_ = 2.0 / nAngleBins_;    

    histogram_.resize(nRBins_);
    avgGofr_.resize(nRBins_);
    for (int i = 0 ; i < nRBins_; ++i) {
        histogram_[i].resize(nAngleBins_);
        avgGofr_[i].resize(nAngleBins_);
    }
}


void GofRAngle::preProcess() {

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

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


void GofRAngle::processHistogram() {

    int nPairs = getNPairs();
    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 GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {

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

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

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

void GofRAngle::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 << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
        rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
        for (int i = 0; i < avgGofr_.size(); ++i) {
            double r = deltaR_ * (i + 0.5);

            for(int j = 0; j < avgGofr_[i].size(); ++j) {
                double cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
                rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
            }

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

    rdfStream.close();
}

double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos2 - pos1;
    currentSnapshot_->wrapVector(r12);
    r12.normalize();
    Vector3d dipole = sd1->getElectroFrame().getColumn(2);
    dipole.normalize();    
    return dot(r12, dipole);
}

double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d v1 = sd1->getElectroFrame().getColumn(2);
    Vector3d v2 = sd2->getElectroFrame().getColumn(2);    
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
}


}


Revision:	2057
Committed:	Mon Feb 21 16:57:22 2005 UTC (19 years, 4 months ago) by tim
File size:	6038 byte(s)
Log Message:	Fix a bug in GofRAngle
#	User	Rev	Content
1	tim	1993	/*
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/GofRAngle.hpp"
45			#include "utils/simError.h"
46
47			namespace oopse {
48
49	tim	2038	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
50			const std::string& sele2, double len, int nrbins, int nangleBins)
51			: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
52	tim	1993
53	tim	2038	deltaR_ = len_ /nRBins_;
54			deltaCosAngle_ = 2.0 / nAngleBins_;
55
56			histogram_.resize(nRBins_);
57			avgGofr_.resize(nRBins_);
58			for (int i = 0 ; i < nRBins_; ++i) {
59			histogram_[i].resize(nAngleBins_);
60			avgGofr_[i].resize(nAngleBins_);
61			}
62	tim	1993	}
63
64
65			void GofRAngle::preProcess() {
66	tim	1994
67			for (int i = 0; i < avgGofr_.size(); ++i) {
68	tim	1993	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
69	tim	1994	}
70	tim	1993	}
71
72			void GofRAngle::initalizeHistogram() {
73			npairs_ = 0;
74			for (int i = 0; i < histogram_.size(); ++i)
75			std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
76			}
77
78
79			void GofRAngle::processHistogram() {
80	tim	2037
81			int nPairs = getNPairs();
82	tim	1993	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
83	tim	2037	double pairDensity = nPairs /volume;
84	tim	1995	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
85	tim	1993
86			for(int i = 0 ; i < histogram_.size(); ++i){
87
88			double rLower = i * deltaR_;
89			double rUpper = rLower + deltaR_;
90			double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
91			double nIdeal = volSlice * pairConstant;
92
93			for (int j = 0; j < histogram_[i].size(); ++j){
94			avgGofr_[i][j] += histogram_[i][j] / nIdeal;
95			}
96			}
97
98			}
99
100			void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
101
102			if (sd1 == sd2) {
103			return;
104			}
105
106			Vector3d pos1 = sd1->getPos();
107			Vector3d pos2 = sd2->getPos();
108	tim	2045	Vector3d r12 = pos2 - pos1;
109	tim	1993	currentSnapshot_->wrapVector(r12);
110
111			double distance = r12.length();
112	tim	1994	int whichRBin = distance / deltaR_;
113	tim	1993
114	tim	2012	if (distance <= len_) {
115			double cosAngle = evaluateAngle(sd1, sd2);
116			double halfBin = (nAngleBins_ - 1) * 0.5;
117			int whichThetaBin = halfBin * (cosAngle + 1.0);
118			++histogram_[whichRBin][whichThetaBin];
119
120			++npairs_;
121			}
122	tim	1993	}
123
124			void GofRAngle::writeRdf() {
125			std::ofstream rdfStream(outputFilename_.c_str());
126			if (rdfStream.is_open()) {
127			rdfStream << "#radial distribution function\n";
128			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
129			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
130	tim	2044	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
131			rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
132	tim	1993	for (int i = 0; i < avgGofr_.size(); ++i) {
133			double r = deltaR_ * (i + 0.5);
134
135			for(int j = 0; j < avgGofr_[i].size(); ++j) {
136	tim	2040	double cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
137	tim	2044	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
138	tim	1993	}
139	tim	2044
140			rdfStream << "\n";
141	tim	1993	}
142
143			} else {
144	tim	2044	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
145			painCave.isFatal = 1;
146			simError();
147	tim	1993	}
148
149			rdfStream.close();
150			}
151
152			double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
153			Vector3d pos1 = sd1->getPos();
154			Vector3d pos2 = sd2->getPos();
155	tim	2045	Vector3d r12 = pos2 - pos1;
156	tim	1993	currentSnapshot_->wrapVector(r12);
157			r12.normalize();
158	tim	1995	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
159	tim	1993	dipole.normalize();
160	tim	1995	return dot(r12, dipole);
161	tim	1993	}
162
163			double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
164			Vector3d v1 = sd1->getElectroFrame().getColumn(2);
165	tim	2057	Vector3d v2 = sd2->getElectroFrame().getColumn(2);
166	tim	1995	v1.normalize();
167			v2.normalize();
168			return dot(v1, v2);
169	tim	1993	}
170
171
172			}
173
174