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, 234107 (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 "primitives/Atom.hpp"
#include "types/MultipoleAdapter.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), evaluator3_(info), 
      seleMan3_(info), doSele3_(false) {
    
    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_);
    }
  }
  
  GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, 
                       const std::string& sele1, 
                       const std::string& sele2, 
                       const std::string& sele3,
                       RealType len, int nrbins, int nangleBins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), 
      nRBins_(nrbins), nAngleBins_(nangleBins), selectionScript3_(sele3),
      evaluator3_(info), seleMan3_(info), doSele3_(true) {

    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_);
    }

    evaluator3_.loadScriptString(sele3);      
    if (!evaluator3_.isDynamic()) {
      seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }

  }
  
  void GofRAngle::processNonOverlapping( SelectionManager& sman1, 
                                         SelectionManager& sman2) {
    StuntDouble* sd1;
    StuntDouble* sd2;
    StuntDouble* sd3;
    int i;    
    int j;
    int k;
    
    // This is the same as a non-overlapping pairwise loop structure:
    // for (int i = 0;  i < ni ; ++i ) {
    //   for (int j = 0; j < nj; ++j) {} 
    // }

    if (doSele3_) {
      if  (evaluator3_.isDynamic()) {
        seleMan3_.setSelectionSet(evaluator3_.evaluate());
      }
      if (sman1.getSelectionCount() != seleMan3_.getSelectionCount() ) {
        RadialDistrFunc::processNonOverlapping( sman1, sman2 );
      }

      for (sd1 = sman1.beginSelected(i), sd3 = seleMan3_.beginSelected(k); 
           sd1 != NULL && sd3 != NULL; 
           sd1 = sman1.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) {
        for (sd2 = sman2.beginSelected(j); sd2 != NULL; 
             sd2 = sman2.nextSelected(j)) {
          collectHistogram(sd1, sd2, sd3);
        }
      }
    } else {
      RadialDistrFunc::processNonOverlapping( sman1, sman2 );
    }
  }

  void GofRAngle::processOverlapping( SelectionManager& sman) {
    StuntDouble* sd1;
    StuntDouble* sd2;
    StuntDouble* sd3;
    int i;    
    int j;
    int k;

    // This is the same as a pairwise loop structure:
    // for (int i = 0;  i < n-1 ; ++i ) {
    //   for (int j = i + 1; j < n; ++j) {} 
    // }
    
    if (doSele3_) {
      if  (evaluator3_.isDynamic()) {
        seleMan3_.setSelectionSet(evaluator3_.evaluate());
      }
      if (sman.getSelectionCount() != seleMan3_.getSelectionCount() ) {
        RadialDistrFunc::processOverlapping( sman);
      }
      for (sd1 = sman.beginSelected(i), sd3 = seleMan3_.beginSelected(k); 
           sd1 != NULL && sd3 != NULL; 
           sd1 = sman.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) {
        for (j  = i, sd2 = sman.nextSelected(j); sd2 != NULL; 
             sd2 = sman.nextSelected(j)) {
          collectHistogram(sd1, sd2, sd3);
        }            
      }
    } else {
      RadialDistrFunc::processOverlapping( sman);
    }    
  }
  

  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 = int(distance / deltaR_);

    if (distance <= len_) {

      RealType cosAngle = evaluateAngle(sd1, sd2);
      RealType halfBin = (nAngleBins_ - 1) * 0.5;
      int whichThetaBin = int(halfBin * (cosAngle + 1.0));
      ++histogram_[whichRBin][whichThetaBin];
        
      ++npairs_;
    }
  }

  void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2, 
                                   StuntDouble* sd3) {

    if (sd1 == sd2) {
      return;
    }

    Vector3d p1 = sd1->getPos();
    Vector3d p3 = sd3->getPos();

    Vector3d c = 0.5 * (p1 + p3);
    Vector3d r13 = p3 - p1;

    Vector3d r12 = sd2->getPos() - c;
  
    if (usePeriodicBoundaryConditions_) {
      currentSnapshot_->wrapVector(r12);
      currentSnapshot_->wrapVector(r13);
    }
    
    RealType distance = r12.length();
    int whichRBin = int(distance / deltaR_);

    if (distance <= len_) {

      RealType cosAngle = evaluateAngle(sd1, sd2, sd3);
      RealType halfBin = (nAngleBins_ - 1) * 0.5;
      int whichThetaBin = int(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_ << ")";
      if (doSele3_) {
        rdfStream << "\tselection3: (" << selectionScript3_ << ")\n";
      } else {
        rdfStream << "\n";
      }
      rdfStream << "#nRBins = " << nRBins_ << "\tmaxLen = " 
                << len_ << "\tdeltaR = " << deltaR_ <<"\n";
      rdfStream << "#nAngleBins =" << nAngleBins_ << "\tdeltaCosAngle = " 
                << 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 vec;    
    
    if (!sd1->isDirectional()) {
      sprintf(painCave.errMsg, 
              "GofRTheta: attempted to use a non-directional object: %s\n", 
              sd1->getType().c_str());
      painCave.isFatal = 1;
      simError();  
    }

    if (sd1->isAtom()) {
      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
      
      if (ma1.isDipole() )
        vec = sd1->getDipole();
      else 
        vec = sd1->getA().transpose() * V3Z;
    } else {
      vec = sd1->getA().transpose() * V3Z;
    }

    vec.normalize();    
      
    return dot(r12, vec);
  }

  RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, 
                                    StuntDouble* sd3) {
    Vector3d p1 = sd1->getPos();
    Vector3d p3 = sd3->getPos();

    Vector3d c = 0.5 * (p1 + p3);
    Vector3d r13 = p3 - p1;

    Vector3d r12 = sd2->getPos() - c;
  
    if (usePeriodicBoundaryConditions_) {
      currentSnapshot_->wrapVector(r12);
      currentSnapshot_->wrapVector(r13);
    }

    r12.normalize();
    r13.normalize();
          
    return dot(r12, r13);
  }

  RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d v1, v2;

    if (!sd1->isDirectional()) {
      sprintf(painCave.errMsg, 
              "GofROmega: attempted to use a non-directional object: %s\n", 
              sd1->getType().c_str());
      painCave.isFatal = 1;
      simError();  
    }

    if (sd1->isAtom()){
      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
      if (ma1.isDipole() )
        v1 = sd1->getDipole();
      else 
        v1 = sd1->getA().transpose() * V3Z;
    } else {
      v1 = sd1->getA().transpose() * V3Z;
    }
    
    if (!sd2->isDirectional()) {
      sprintf(painCave.errMsg, 
              "GofROmega attempted to use a non-directional object: %s\n", 
              sd2->getType().c_str());
      painCave.isFatal = 1;
      simError();  
    }

    if (sd2->isAtom()) {
      AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
      MultipoleAdapter ma2 = MultipoleAdapter(atype2);
           
      if (ma2.isDipole() )
        v2 = sd2->getDipole();
      else 
        v2 = sd2->getA().transpose() * V3Z;
    } else {
      v2 = sd2->getA().transpose() * V3Z;
    }
      
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
  }

  RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, 
                                    StuntDouble* sd3) {

    Vector3d v1;
    Vector3d v2;
    
    v1 = sd3->getPos() - sd1->getPos();
    if (usePeriodicBoundaryConditions_) 
      currentSnapshot_->wrapVector(v1);
    
    if (!sd2->isDirectional()) {
      sprintf(painCave.errMsg, 
              "GofROmega: attempted to use a non-directional object: %s\n", 
              sd2->getType().c_str());
      painCave.isFatal = 1;
      simError();  
    }

    if (sd2->isAtom()) {
      AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
      MultipoleAdapter ma2 = MultipoleAdapter(atype2);
           
      if (ma2.isDipole() )
        v2 = sd2->getDipole();
      else 
        v2 = sd2->getA().transpose() * V3Z;
    } else {
      v2 = sd2->getA().transpose() * V3Z;
    }
      
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
  }
}


Revision:	2023
Committed:	Thu Oct 2 14:35:14 2014 UTC (11 years, 1 month ago) by gezelter
File size:	13552 byte(s)
Log Message:	Added 3rd selection option for the 2d g(r) analyzers
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1879	#include "primitives/Atom.hpp"
47			#include "types/MultipoleAdapter.hpp"
48	tim	309	#include "utils/simError.h"
49
50	gezelter	1390	namespace OpenMD {
51	gezelter	2023
52			GofRAngle::GofRAngle(SimInfo* info, const std::string& filename,
53			const std::string& sele1,
54			const std::string& sele2,
55			RealType len, int nrbins, int nangleBins)
56			: RadialDistrFunc(info, filename, sele1, sele2), len_(len),
57			nRBins_(nrbins), nAngleBins_(nangleBins), evaluator3_(info),
58			seleMan3_(info), doSele3_(false) {
59
60			deltaR_ = len_ /(double) nRBins_;
61			deltaCosAngle_ = 2.0 / (double)nAngleBins_;
62			histogram_.resize(nRBins_);
63			avgGofr_.resize(nRBins_);
64			for (int i = 0 ; i < nRBins_; ++i) {
65			histogram_[i].resize(nAngleBins_);
66			avgGofr_[i].resize(nAngleBins_);
67			}
68			}
69
70			GofRAngle::GofRAngle(SimInfo* info, const std::string& filename,
71			const std::string& sele1,
72			const std::string& sele2,
73			const std::string& sele3,
74			RealType len, int nrbins, int nangleBins)
75			: RadialDistrFunc(info, filename, sele1, sele2), len_(len),
76			nRBins_(nrbins), nAngleBins_(nangleBins), selectionScript3_(sele3),
77			evaluator3_(info), seleMan3_(info), doSele3_(true) {
78	tim	309
79	gezelter	2023	deltaR_ = len_ /(double) nRBins_;
80			deltaCosAngle_ = 2.0 / (double)nAngleBins_;
81			histogram_.resize(nRBins_);
82			avgGofr_.resize(nRBins_);
83			for (int i = 0 ; i < nRBins_; ++i) {
84			histogram_[i].resize(nAngleBins_);
85			avgGofr_[i].resize(nAngleBins_);
86			}
87	tim	309
88	gezelter	2023	evaluator3_.loadScriptString(sele3);
89			if (!evaluator3_.isDynamic()) {
90			seleMan3_.setSelectionSet(evaluator3_.evaluate());
91			}
92
93			}
94
95			void GofRAngle::processNonOverlapping( SelectionManager& sman1,
96			SelectionManager& sman2) {
97			StuntDouble* sd1;
98			StuntDouble* sd2;
99			StuntDouble* sd3;
100			int i;
101			int j;
102			int k;
103
104			// This is the same as a non-overlapping pairwise loop structure:
105			// for (int i = 0; i < ni ; ++i ) {
106			// for (int j = 0; j < nj; ++j) {}
107			// }
108
109			if (doSele3_) {
110			if (evaluator3_.isDynamic()) {
111			seleMan3_.setSelectionSet(evaluator3_.evaluate());
112	gezelter	507	}
113	gezelter	2023	if (sman1.getSelectionCount() != seleMan3_.getSelectionCount() ) {
114			RadialDistrFunc::processNonOverlapping( sman1, sman2 );
115			}
116
117			for (sd1 = sman1.beginSelected(i), sd3 = seleMan3_.beginSelected(k);
118			sd1 != NULL && sd3 != NULL;
119			sd1 = sman1.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) {
120			for (sd2 = sman2.beginSelected(j); sd2 != NULL;
121			sd2 = sman2.nextSelected(j)) {
122			collectHistogram(sd1, sd2, sd3);
123			}
124			}
125			} else {
126			RadialDistrFunc::processNonOverlapping( sman1, sman2 );
127	tim	354	}
128	gezelter	2023	}
129	tim	309
130	gezelter	2023	void GofRAngle::processOverlapping( SelectionManager& sman) {
131			StuntDouble* sd1;
132			StuntDouble* sd2;
133			StuntDouble* sd3;
134			int i;
135			int j;
136			int k;
137	tim	309
138	gezelter	2023	// This is the same as a pairwise loop structure:
139			// for (int i = 0; i < n-1 ; ++i ) {
140			// for (int j = i + 1; j < n; ++j) {}
141			// }
142
143			if (doSele3_) {
144			if (evaluator3_.isDynamic()) {
145			seleMan3_.setSelectionSet(evaluator3_.evaluate());
146			}
147			if (sman.getSelectionCount() != seleMan3_.getSelectionCount() ) {
148			RadialDistrFunc::processOverlapping( sman);
149			}
150			for (sd1 = sman.beginSelected(i), sd3 = seleMan3_.beginSelected(k);
151			sd1 != NULL && sd3 != NULL;
152			sd1 = sman.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) {
153			for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL;
154			sd2 = sman.nextSelected(j)) {
155			collectHistogram(sd1, sd2, sd3);
156			}
157			}
158			} else {
159			RadialDistrFunc::processOverlapping( sman);
160			}
161			}
162
163
164	gezelter	507	void GofRAngle::preProcess() {
165	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
166	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
167	tim	310	}
168	gezelter	507	}
169	tim	309
170	jmichalk	1785	void GofRAngle::initializeHistogram() {
171	tim	309	npairs_ = 0;
172	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i){
173	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
174	xsun	1213	}
175	gezelter	507	}
176	tim	309
177	gezelter	507	void GofRAngle::processHistogram() {
178	tim	353	int nPairs = getNPairs();
179	tim	963	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
180			RealType pairDensity = nPairs /volume;
181			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
182	tim	309
183	gezelter	1782	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
184	tim	309
185	tim	963	RealType rLower = i * deltaR_;
186			RealType rUpper = rLower + deltaR_;
187	gezelter	2023	RealType volSlice = ( rUpper * rUpper * rUpper ) -
188			( rLower * rLower * rLower );
189	tim	963	RealType nIdeal = volSlice * pairConstant;
190	tim	309
191	gezelter	1782	for (unsigned int j = 0; j < histogram_[i].size(); ++j){
192	gezelter	507	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
193			}
194	tim	309	}
195
196	gezelter	507	}
197	tim	309
198	gezelter	507	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
199	tim	309
200			if (sd1 == sd2) {
201	gezelter	507	return;
202	tim	309	}
203			Vector3d pos1 = sd1->getPos();
204			Vector3d pos2 = sd2->getPos();
205	tim	361	Vector3d r12 = pos2 - pos1;
206	gezelter	1078	if (usePeriodicBoundaryConditions_)
207			currentSnapshot_->wrapVector(r12);
208	tim	309
209	tim	963	RealType distance = r12.length();
210	gezelter	1790	int whichRBin = int(distance / deltaR_);
211	tim	309
212	tim	328	if (distance <= len_) {
213	xsun	1213
214	tim	963	RealType cosAngle = evaluateAngle(sd1, sd2);
215			RealType halfBin = (nAngleBins_ - 1) * 0.5;
216	gezelter	1790	int whichThetaBin = int(halfBin * (cosAngle + 1.0));
217	gezelter	507	++histogram_[whichRBin][whichThetaBin];
218	tim	328
219	gezelter	507	++npairs_;
220	tim	328	}
221	gezelter	507	}
222	tim	309
223	gezelter	2023	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2,
224			StuntDouble* sd3) {
225
226			if (sd1 == sd2) {
227			return;
228			}
229
230			Vector3d p1 = sd1->getPos();
231			Vector3d p3 = sd3->getPos();
232
233			Vector3d c = 0.5 * (p1 + p3);
234			Vector3d r13 = p3 - p1;
235
236			Vector3d r12 = sd2->getPos() - c;
237
238			if (usePeriodicBoundaryConditions_) {
239			currentSnapshot_->wrapVector(r12);
240			currentSnapshot_->wrapVector(r13);
241			}
242
243			RealType distance = r12.length();
244			int whichRBin = int(distance / deltaR_);
245
246			if (distance <= len_) {
247
248			RealType cosAngle = evaluateAngle(sd1, sd2, sd3);
249			RealType halfBin = (nAngleBins_ - 1) * 0.5;
250			int whichThetaBin = int(halfBin * (cosAngle + 1.0));
251			++histogram_[whichRBin][whichThetaBin];
252
253			++npairs_;
254			}
255			}
256
257	gezelter	507	void GofRAngle::writeRdf() {
258	tim	309	std::ofstream rdfStream(outputFilename_.c_str());
259			if (rdfStream.is_open()) {
260	gezelter	507	rdfStream << "#radial distribution function\n";
261			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
262	gezelter	2023	rdfStream << "selection2: (" << selectionScript2_ << ")";
263			if (doSele3_) {
264			rdfStream << "\tselection3: (" << selectionScript3_ << ")\n";
265			} else {
266			rdfStream << "\n";
267			}
268			rdfStream << "#nRBins = " << nRBins_ << "\tmaxLen = "
269			<< len_ << "\tdeltaR = " << deltaR_ <<"\n";
270			rdfStream << "#nAngleBins =" << nAngleBins_ << "\tdeltaCosAngle = "
271			<< deltaCosAngle_ << "\n";
272	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
273	gezelter	1796	// RealType r = deltaR_ * (i + 0.5);
274	tim	309
275	gezelter	1782	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
276	gezelter	1796	// RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
277	gezelter	507	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
278			}
279	tim	360
280	gezelter	507	rdfStream << "\n";
281			}
282	tim	309
283			} else {
284	gezelter	2023	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n",
285			outputFilename_.c_str());
286	gezelter	507	painCave.isFatal = 1;
287			simError();
288	tim	309	}
289
290			rdfStream.close();
291	gezelter	507	}
292	tim	309
293	tim	963	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
294	tim	309	Vector3d pos1 = sd1->getPos();
295			Vector3d pos2 = sd2->getPos();
296	tim	361	Vector3d r12 = pos2 - pos1;
297	xsun	1213
298	gezelter	1078	if (usePeriodicBoundaryConditions_)
299			currentSnapshot_->wrapVector(r12);
300
301	tim	309	r12.normalize();
302	gezelter	1879
303	gezelter	1968	Vector3d vec;
304
305	gezelter	2023	if (!sd1->isDirectional()) {
306			sprintf(painCave.errMsg,
307			"GofRTheta: attempted to use a non-directional object: %s\n",
308			sd1->getType().c_str());
309			painCave.isFatal = 1;
310			simError();
311			}
312
313	gezelter	1968	if (sd1->isAtom()) {
314			AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
315			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
316
317			if (ma1.isDipole() )
318			vec = sd1->getDipole();
319			else
320			vec = sd1->getA().transpose() * V3Z;
321			} else {
322	gezelter	1879	vec = sd1->getA().transpose() * V3Z;
323	gezelter	1968	}
324
325	gezelter	1879	vec.normalize();
326	gezelter	1968
327	gezelter	1879	return dot(r12, vec);
328	gezelter	507	}
329	tim	309
330	gezelter	2023	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
331			StuntDouble* sd3) {
332			Vector3d p1 = sd1->getPos();
333			Vector3d p3 = sd3->getPos();
334
335			Vector3d c = 0.5 * (p1 + p3);
336			Vector3d r13 = p3 - p1;
337
338			Vector3d r12 = sd2->getPos() - c;
339
340			if (usePeriodicBoundaryConditions_) {
341			currentSnapshot_->wrapVector(r12);
342			currentSnapshot_->wrapVector(r13);
343			}
344
345			r12.normalize();
346			r13.normalize();
347
348			return dot(r12, r13);
349			}
350
351	tim	963	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
352	gezelter	1879	Vector3d v1, v2;
353
354	gezelter	2023	if (!sd1->isDirectional()) {
355			sprintf(painCave.errMsg,
356			"GofROmega: attempted to use a non-directional object: %s\n",
357			sd1->getType().c_str());
358			painCave.isFatal = 1;
359			simError();
360			}
361
362	gezelter	1968	if (sd1->isAtom()){
363			AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
364			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
365			if (ma1.isDipole() )
366			v1 = sd1->getDipole();
367			else
368			v1 = sd1->getA().transpose() * V3Z;
369			} else {
370	gezelter	1879	v1 = sd1->getA().transpose() * V3Z;
371	gezelter	1968	}
372
373	gezelter	2023	if (!sd2->isDirectional()) {
374			sprintf(painCave.errMsg,
375			"GofROmega attempted to use a non-directional object: %s\n",
376			sd2->getType().c_str());
377			painCave.isFatal = 1;
378			simError();
379			}
380
381	gezelter	1968	if (sd2->isAtom()) {
382			AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
383			MultipoleAdapter ma2 = MultipoleAdapter(atype2);
384
385			if (ma2.isDipole() )
386			v2 = sd2->getDipole();
387			else
388			v2 = sd2->getA().transpose() * V3Z;
389			} else {
390	gezelter	1879	v2 = sd2->getA().transpose() * V3Z;
391	gezelter	1968	}
392
393	tim	311	v1.normalize();
394			v2.normalize();
395			return dot(v1, v2);
396	gezelter	507	}
397	tim	309
398	gezelter	2023	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
399			StuntDouble* sd3) {
400	tim	309
401	gezelter	2023	Vector3d v1;
402			Vector3d v2;
403
404			v1 = sd3->getPos() - sd1->getPos();
405			if (usePeriodicBoundaryConditions_)
406			currentSnapshot_->wrapVector(v1);
407
408			if (!sd2->isDirectional()) {
409			sprintf(painCave.errMsg,
410			"GofROmega: attempted to use a non-directional object: %s\n",
411			sd2->getType().c_str());
412			painCave.isFatal = 1;
413			simError();
414			}
415
416			if (sd2->isAtom()) {
417			AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
418			MultipoleAdapter ma2 = MultipoleAdapter(atype2);
419
420			if (ma2.isDipole() )
421			v2 = sd2->getDipole();
422			else
423			v2 = sd2->getA().transpose() * V3Z;
424			} else {
425			v2 = sd2->getA().transpose() * V3Z;
426			}
427
428			v1.normalize();
429			v2.normalize();
430			return dot(v1, v2);
431			}
432	tim	309	}
433
434