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 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 = 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:	2037
Committed:	Wed Feb 16 19:36:30 2005 UTC (19 years, 5 months ago) by tim
File size:	5352 byte(s)
Log Message:	change the suffix of output files;fix the problem of counting in staticProps
#	Content
1	/*
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	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50	: RadialDistrFunc(info, filename, sele1, sele2){
51
52	}
53
54
55	void GofRAngle::preProcess() {
56
57	for (int i = 0; i < avgGofr_.size(); ++i) {
58	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
59	}
60	}
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
71	int nPairs = getNPairs();
72	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
73	double pairDensity = nPairs /volume;
74	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
75
76	for(int i = 0 ; i < histogram_.size(); ++i){
77
78	double rLower = i * deltaR_;
79	double rUpper = rLower + deltaR_;
80	double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
81	double nIdeal = volSlice * pairConstant;
82
83	for (int j = 0; j < histogram_[i].size(); ++j){
84	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
85	}
86	}
87
88	}
89
90	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
91
92	if (sd1 == sd2) {
93	return;
94	}
95
96	Vector3d pos1 = sd1->getPos();
97	Vector3d pos2 = sd2->getPos();
98	Vector3d r12 = pos1 - pos2;
99	currentSnapshot_->wrapVector(r12);
100
101	double distance = r12.length();
102	int whichRBin = distance / deltaR_;
103
104	if (distance <= len_) {
105	double cosAngle = evaluateAngle(sd1, sd2);
106	double halfBin = (nAngleBins_ - 1) * 0.5;
107	int whichThetaBin = halfBin * (cosAngle + 1.0);
108	++histogram_[whichRBin][whichThetaBin];
109
110	++npairs_;
111	}
112	}
113
114	void GofRAngle::writeRdf() {
115	std::ofstream rdfStream(outputFilename_.c_str());
116	if (rdfStream.is_open()) {
117	rdfStream << "#radial distribution function\n";
118	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
119	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
120	rdfStream << "#r\tcorrValue\n";
121	for (int i = 0; i < avgGofr_.size(); ++i) {
122	double r = deltaR_ * (i + 0.5);
123
124	for(int j = 0; j < avgGofr_[i].size(); ++j) {
125	double cosAngle = -1.0 + (i + 0.5)*deltaCosAngle_;
126	rdfStream << r << "\t" << cosAngle << "\t" << avgGofr_[i][j]/nProcessed_ << "\n";
127	}
128	}
129
130	} else {
131
132
133	}
134
135	rdfStream.close();
136	}
137
138	double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
139	Vector3d pos1 = sd1->getPos();
140	Vector3d pos2 = sd2->getPos();
141	Vector3d r12 = pos1 - pos2;
142	currentSnapshot_->wrapVector(r12);
143	r12.normalize();
144	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
145	dipole.normalize();
146	return dot(r12, dipole);
147	}
148
149	double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
150	Vector3d v1 = sd1->getElectroFrame().getColumn(2);
151	Vector3d v2 = sd1->getElectroFrame().getColumn(2);
152	v1.normalize();
153	v2.normalize();
154	return dot(v1, v2);
155	}
156
157
158	}
159
160