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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

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

  void GofRAngle::initializeHistogram() {
    npairs_ = 0;
    for (unsigned 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(unsigned 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 (unsigned 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 (unsigned int i = 0; i < avgGofr_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);

        for(unsigned 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:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	6244 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	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	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	309	*/
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/GofRAngle.hpp"
46			#include "utils/simError.h"
47
48	gezelter	1390	namespace OpenMD {
49	tim	309
50	gezelter	507	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
51	tim	963	const std::string& sele2, RealType len, int nrbins, int nangleBins)
52	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
53	tim	309
54	xsun	1213	deltaR_ = len_ /(double) nRBins_;
55			deltaCosAngle_ = 2.0 / (double)nAngleBins_;
56	gezelter	507	histogram_.resize(nRBins_);
57			avgGofr_.resize(nRBins_);
58			for (int i = 0 ; i < nRBins_; ++i) {
59	tim	354	histogram_[i].resize(nAngleBins_);
60			avgGofr_[i].resize(nAngleBins_);
61	gezelter	507	}
62	tim	354	}
63	tim	309
64
65	gezelter	507	void GofRAngle::preProcess() {
66	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
67	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
68	tim	310	}
69	gezelter	507	}
70	tim	309
71	jmichalk	1785	void GofRAngle::initializeHistogram() {
72	tim	309	npairs_ = 0;
73	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i){
74	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
75	xsun	1213	}
76	gezelter	507	}
77	tim	309
78	gezelter	507	void GofRAngle::processHistogram() {
79	tim	353	int nPairs = getNPairs();
80	tim	963	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
81			RealType pairDensity = nPairs /volume;
82			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
83	tim	309
84	gezelter	1782	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
85	tim	309
86	tim	963	RealType rLower = i * deltaR_;
87			RealType rUpper = rLower + deltaR_;
88			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
89			RealType nIdeal = volSlice * pairConstant;
90	tim	309
91	gezelter	1782	for (unsigned int j = 0; j < histogram_[i].size(); ++j){
92	gezelter	507	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
93			}
94	tim	309	}
95
96	gezelter	507	}
97	tim	309
98	gezelter	507	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
99	tim	309
100			if (sd1 == sd2) {
101	gezelter	507	return;
102	tim	309	}
103			Vector3d pos1 = sd1->getPos();
104			Vector3d pos2 = sd2->getPos();
105	tim	361	Vector3d r12 = pos2 - pos1;
106	gezelter	1078	if (usePeriodicBoundaryConditions_)
107			currentSnapshot_->wrapVector(r12);
108	tim	309
109	tim	963	RealType distance = r12.length();
110	tim	310	int whichRBin = distance / deltaR_;
111	tim	309
112	tim	328	if (distance <= len_) {
113	xsun	1213
114	tim	963	RealType cosAngle = evaluateAngle(sd1, sd2);
115			RealType halfBin = (nAngleBins_ - 1) * 0.5;
116	gezelter	507	int whichThetaBin = halfBin * (cosAngle + 1.0);
117			++histogram_[whichRBin][whichThetaBin];
118	tim	328
119	gezelter	507	++npairs_;
120	tim	328	}
121	gezelter	507	}
122	tim	309
123	gezelter	507	void GofRAngle::writeRdf() {
124	tim	309	std::ofstream rdfStream(outputFilename_.c_str());
125			if (rdfStream.is_open()) {
126	gezelter	507	rdfStream << "#radial distribution function\n";
127			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
128			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
129			rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
130			rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
131	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
132	tim	963	RealType r = deltaR_ * (i + 0.5);
133	tim	309
134	gezelter	1782	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
135	tim	963	RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
136	gezelter	507	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
137			}
138	tim	360
139	gezelter	507	rdfStream << "\n";
140			}
141	tim	309
142			} else {
143	gezelter	507	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
144			painCave.isFatal = 1;
145			simError();
146	tim	309	}
147
148			rdfStream.close();
149	gezelter	507	}
150	tim	309
151	tim	963	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
152	tim	309	Vector3d pos1 = sd1->getPos();
153			Vector3d pos2 = sd2->getPos();
154	tim	361	Vector3d r12 = pos2 - pos1;
155	xsun	1213
156	gezelter	1078	if (usePeriodicBoundaryConditions_)
157			currentSnapshot_->wrapVector(r12);
158
159	tim	309	r12.normalize();
160	tim	311	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
161	tim	309	dipole.normalize();
162	tim	311	return dot(r12, dipole);
163	gezelter	507	}
164	tim	309
165	tim	963	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
166	tim	309	Vector3d v1 = sd1->getElectroFrame().getColumn(2);
167	tim	373	Vector3d v2 = sd2->getElectroFrame().getColumn(2);
168	tim	311	v1.normalize();
169			v2.normalize();
170			return dot(v1, v2);
171	gezelter	507	}
172	tim	309
173
174			}
175
176