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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	5960 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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,
50	const std::string& sele2, double len, int nrbins, int nangleBins)
51	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
52
53	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	}
63
64
65	void GofRAngle::preProcess() {
66
67	for (int i = 0; i < avgGofr_.size(); ++i) {
68	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
69	}
70	}
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
81	int nPairs = getNPairs();
82	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
83	double pairDensity = nPairs /volume;
84	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
85
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	Vector3d r12 = pos2 - pos1;
109	currentSnapshot_->wrapVector(r12);
110
111	double distance = r12.length();
112	int whichRBin = distance / deltaR_;
113
114	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	}
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	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
131	rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
132	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	double cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
137	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
138	}
139
140	rdfStream << "\n";
141	}
142
143	} else {
144	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
145	painCave.isFatal = 1;
146	simError();
147	}
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	Vector3d r12 = pos2 - pos1;
156	currentSnapshot_->wrapVector(r12);
157	r12.normalize();
158	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
159	dipole.normalize();
160	return dot(r12, dipole);
161	}
162
163	double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
164	Vector3d v1 = sd1->getElectroFrame().getColumn(2);
165	Vector3d v2 = sd2->getElectroFrame().getColumn(2);
166	v1.normalize();
167	v2.normalize();
168	return dot(v1, v2);
169	}
170
171
172	}
173
174