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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/GofRAngle.hpp"
#include "utils/simError.h"

namespace OpenMD {

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

      deltaR_ = len_ /(double) nRBins_;
      deltaCosAngle_ = 2.0 / (double)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();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs /volume;
    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;

    for(int i = 0 ; i < histogram_.size(); ++i){

      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
      RealType 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;
    if (usePeriodicBoundaryConditions_)
      currentSnapshot_->wrapVector(r12);

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

    if (distance <= len_) {

      RealType cosAngle = evaluateAngle(sd1, sd2);
      RealType 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) {
        RealType r = deltaR_ * (i + 0.5);

        for(int j = 0; j < avgGofr_[i].size(); ++j) {
          RealType 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();
  }

  RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos2 - pos1;
  
    if (usePeriodicBoundaryConditions_)
      currentSnapshot_->wrapVector(r12);

    r12.normalize();
    Vector3d dipole = sd1->getElectroFrame().getColumn(2);
    dipole.normalize();    
    return dot(r12, dipole);
  }

  RealType 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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/applications/staticProps/GofRAngle.cpp*
File size:	6123 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	tim	309	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	309	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	309	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	309	*/
41
42			#include <algorithm>
43			#include <fstream>
44			#include "applications/staticProps/GofRAngle.hpp"
45			#include "utils/simError.h"
46
47	gezelter	1390	namespace OpenMD {
48	tim	309
49	gezelter	507	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
50	tim	963	const std::string& sele2, RealType len, int nrbins, int nangleBins)
51	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
52	tim	309
53	xsun	1213	deltaR_ = len_ /(double) nRBins_;
54			deltaCosAngle_ = 2.0 / (double)nAngleBins_;
55	gezelter	507	histogram_.resize(nRBins_);
56			avgGofr_.resize(nRBins_);
57			for (int i = 0 ; i < nRBins_; ++i) {
58	tim	354	histogram_[i].resize(nAngleBins_);
59			avgGofr_[i].resize(nAngleBins_);
60	gezelter	507	}
61	tim	354	}
62	tim	309
63
64	gezelter	507	void GofRAngle::preProcess() {
65	tim	310	for (int i = 0; i < avgGofr_.size(); ++i) {
66	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
67	tim	310	}
68	gezelter	507	}
69	tim	309
70	gezelter	507	void GofRAngle::initalizeHistogram() {
71	tim	309	npairs_ = 0;
72	xsun	1213	for (int i = 0; i < histogram_.size(); ++i){
73	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
74	xsun	1213	}
75	gezelter	507	}
76	tim	309
77	gezelter	507	void GofRAngle::processHistogram() {
78	tim	353	int nPairs = getNPairs();
79	tim	963	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
80			RealType pairDensity = nPairs /volume;
81			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
82	tim	309
83			for(int i = 0 ; i < histogram_.size(); ++i){
84
85	tim	963	RealType rLower = i * deltaR_;
86			RealType rUpper = rLower + deltaR_;
87			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
88			RealType nIdeal = volSlice * pairConstant;
89	tim	309
90	gezelter	507	for (int j = 0; j < histogram_[i].size(); ++j){
91			avgGofr_[i][j] += histogram_[i][j] / nIdeal;
92			}
93	tim	309	}
94
95	gezelter	507	}
96	tim	309
97	gezelter	507	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
98	tim	309
99			if (sd1 == sd2) {
100	gezelter	507	return;
101	tim	309	}
102			Vector3d pos1 = sd1->getPos();
103			Vector3d pos2 = sd2->getPos();
104	tim	361	Vector3d r12 = pos2 - pos1;
105	gezelter	1078	if (usePeriodicBoundaryConditions_)
106			currentSnapshot_->wrapVector(r12);
107	tim	309
108	tim	963	RealType distance = r12.length();
109	tim	310	int whichRBin = distance / deltaR_;
110	tim	309
111	tim	328	if (distance <= len_) {
112	xsun	1213
113	tim	963	RealType cosAngle = evaluateAngle(sd1, sd2);
114			RealType halfBin = (nAngleBins_ - 1) * 0.5;
115	gezelter	507	int whichThetaBin = halfBin * (cosAngle + 1.0);
116			++histogram_[whichRBin][whichThetaBin];
117	tim	328
118	gezelter	507	++npairs_;
119	tim	328	}
120	gezelter	507	}
121	tim	309
122	gezelter	507	void GofRAngle::writeRdf() {
123	tim	309	std::ofstream rdfStream(outputFilename_.c_str());
124			if (rdfStream.is_open()) {
125	gezelter	507	rdfStream << "#radial distribution function\n";
126			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
127			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
128			rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
129			rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
130			for (int i = 0; i < avgGofr_.size(); ++i) {
131	tim	963	RealType r = deltaR_ * (i + 0.5);
132	tim	309
133	gezelter	507	for(int j = 0; j < avgGofr_[i].size(); ++j) {
134	tim	963	RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
135	gezelter	507	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
136			}
137	tim	360
138	gezelter	507	rdfStream << "\n";
139			}
140	tim	309
141			} else {
142	gezelter	507	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
143			painCave.isFatal = 1;
144			simError();
145	tim	309	}
146
147			rdfStream.close();
148	gezelter	507	}
149	tim	309
150	tim	963	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
151	tim	309	Vector3d pos1 = sd1->getPos();
152			Vector3d pos2 = sd2->getPos();
153	tim	361	Vector3d r12 = pos2 - pos1;
154	xsun	1213
155	gezelter	1078	if (usePeriodicBoundaryConditions_)
156			currentSnapshot_->wrapVector(r12);
157
158	tim	309	r12.normalize();
159	tim	311	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
160	tim	309	dipole.normalize();
161	tim	311	return dot(r12, dipole);
162	gezelter	507	}
163	tim	309
164	tim	963	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
165	tim	309	Vector3d v1 = sd1->getElectroFrame().getColumn(2);
166	tim	373	Vector3d v2 = sd2->getElectroFrame().getColumn(2);
167	tim	311	v1.normalize();
168			v2.normalize();
169			return dot(v1, v2);
170	gezelter	507	}
171	tim	309
172
173			}
174
175