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)
    : RadialDistrFunc(info, filename, sele1, sele2){

}


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 nRealPairs = getNRealPairs();
    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    double pairDensity = nRealPairs /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 = pos1 - pos2;
    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 << "#r\tcorrValue\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 + (i + 0.5)*deltaCosAngle_;
                rdfStream << r << "\t" << cosAngle << "\t" << avgGofr_[i][j]/nProcessed_ << "\n";
            }
        }
        
    } else {


    }

    rdfStream.close();
}

double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos1 - pos2;
    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 = sd1->getElectroFrame().getColumn(2);    
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
}


}


Revision:	2032
Committed:	Tue Feb 15 17:24:12 2005 UTC (19 years, 4 months ago) by tim
File size:	5363 byte(s)
Log Message:	bug fix in StaticProps
#	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	1994	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50			: RadialDistrFunc(info, filename, sele1, sele2){
51	tim	1993
52			}
53
54
55			void GofRAngle::preProcess() {
56	tim	1994
57			for (int i = 0; i < avgGofr_.size(); ++i) {
58	tim	1993	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
59	tim	1994	}
60	tim	1993	}
61
62			void GofRAngle::initalizeHistogram() {
63			npairs_ = 0;
64			for (int i = 0; i < histogram_.size(); ++i)
65			std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
66			}
67
68
69			void GofRAngle::processHistogram() {
70	tim	2032	int nRealPairs = getNRealPairs();
71	tim	1993	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
72	tim	2032	double pairDensity = nRealPairs /volume;
73	tim	1995	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
74	tim	1993
75			for(int i = 0 ; i < histogram_.size(); ++i){
76
77			double rLower = i * deltaR_;
78			double rUpper = rLower + deltaR_;
79			double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
80			double nIdeal = volSlice * pairConstant;
81
82			for (int j = 0; j < histogram_[i].size(); ++j){
83			avgGofr_[i][j] += histogram_[i][j] / nIdeal;
84			}
85			}
86
87			}
88
89			void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
90
91			if (sd1 == sd2) {
92			return;
93			}
94
95			Vector3d pos1 = sd1->getPos();
96			Vector3d pos2 = sd2->getPos();
97			Vector3d r12 = pos1 - pos2;
98			currentSnapshot_->wrapVector(r12);
99
100			double distance = r12.length();
101	tim	1994	int whichRBin = distance / deltaR_;
102	tim	1993
103	tim	2012	if (distance <= len_) {
104			double cosAngle = evaluateAngle(sd1, sd2);
105			double halfBin = (nAngleBins_ - 1) * 0.5;
106			int whichThetaBin = halfBin * (cosAngle + 1.0);
107			++histogram_[whichRBin][whichThetaBin];
108
109			++npairs_;
110			}
111	tim	1993	}
112
113			void GofRAngle::writeRdf() {
114			std::ofstream rdfStream(outputFilename_.c_str());
115			if (rdfStream.is_open()) {
116			rdfStream << "#radial distribution function\n";
117			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
118			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
119			rdfStream << "#r\tcorrValue\n";
120			for (int i = 0; i < avgGofr_.size(); ++i) {
121			double r = deltaR_ * (i + 0.5);
122
123			for(int j = 0; j < avgGofr_[i].size(); ++j) {
124	tim	1994	double cosAngle = -1.0 + (i + 0.5)*deltaCosAngle_;
125	tim	1993	rdfStream << r << "\t" << cosAngle << "\t" << avgGofr_[i][j]/nProcessed_ << "\n";
126			}
127			}
128
129			} else {
130
131
132			}
133
134			rdfStream.close();
135			}
136
137			double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
138			Vector3d pos1 = sd1->getPos();
139			Vector3d pos2 = sd2->getPos();
140			Vector3d r12 = pos1 - pos2;
141			currentSnapshot_->wrapVector(r12);
142			r12.normalize();
143	tim	1995	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
144	tim	1993	dipole.normalize();
145	tim	1995	return dot(r12, dipole);
146	tim	1993	}
147
148			double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
149			Vector3d v1 = sd1->getElectroFrame().getColumn(2);
150	tim	1994	Vector3d v2 = sd1->getElectroFrame().getColumn(2);
151	tim	1995	v1.normalize();
152			v2.normalize();
153			return dot(v1, v2);
154	tim	1993	}
155
156
157			}
158
159