applications/staticProps/SpatialStatistics.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 "applications/staticProps/SpatialStatistics.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"

namespace OpenMD {
  
  SpatialStatistics::SpatialStatistics(SimInfo* info, const string& filename, 
                                       const string& sele, int nbins)
    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info),
      seleMan_(info), nBins_(nbins){
    
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    // Pre-load an OutputData for the count of objects:
    counts_ = new OutputData;
    counts_->units =  "objects";
    counts_->title =  "Objects";
    counts_->dataType = odtReal;
    counts_->dataHandling = odhTotal;
    counts_->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      counts_->accumulator.push_back( new Accumulator() );
    
    setOutputName(getPrefix(filename) + ".spst");
  }

  SpatialStatistics::~SpatialStatistics() {
    vector<OutputData*>::iterator i;
    OutputData* outputData;
    
    for(outputData = beginOutputData(i); outputData; 
        outputData = nextOutputData(i)) {
      delete outputData;
    }
    data_.clear();

    delete counts_;
  }


  void SpatialStatistics::process() {

    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames/step_;

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      processFrame(istep);
    }
    writeOutput();
  }


  void SpatialStatistics::processFrame(int istep) {
    Molecule* mol;
    RigidBody* rb;
    StuntDouble* sd;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    int i;
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      
      // change the positions of atoms which belong to the rigidbodies
      
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        rb->updateAtoms();
      }
    }
    
    if (evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    // loop over the selected atoms:
    
    for (sd = seleMan_.beginSelected(i); sd != NULL; 
         sd = seleMan_.nextSelected(i)) {
      
      // figure out where that object is:
      
      Vector3d pos = sd->getPos();
      
      int bin = getBin(pos);
      
      // forward the work of statistics on to the subclass:
      
      processStuntDouble( sd, bin );

      dynamic_cast<Accumulator *>(counts_->accumulator[bin])->add(1);
    }      
  }
  

  void SpatialStatistics::writeOutput() {
    
    vector<OutputData*>::iterator i;
    OutputData* outputData;
    
    ofstream outStream(outputFilename_.c_str());
    if (outStream.is_open()) {
      
      //write title
      outStream << "# SPATIAL STATISTICS\n";
      outStream << "#";
      
      for(outputData = beginOutputData(i); outputData; 
          outputData = nextOutputData(i)) {
        outStream << "\t" << outputData->title << 
          "(" << outputData->units << ")";
        // add some extra tabs for column alignment
        if (outputData->dataType == odtVector3) outStream << "\t\t";
      }
      
      outStream << std::endl;
      
      outStream.precision(8);
      
      for (int j = 0; j < nBins_; j++) {        
        
        int counts = counts_->accumulator[j]->count();

        if (counts > 0) {
          for(outputData = beginOutputData(i); outputData; 
              outputData = nextOutputData(i)) {
            
            int n = outputData->accumulator[j]->count();
            if (n != 0) {
              writeData( outStream, outputData, j );
            }
          }
          outStream << std::endl;
        }
      }
        
      outStream << "#######################################################\n";
      outStream << "# Standard Deviations in those quantities follow:\n";
      outStream << "#######################################################\n";
      
      for (int j = 0; j < nBins_; j++) {
        int counts = counts_->accumulator[j]->count();
        if (counts > 0) {
          
          outStream << "#";
          for(outputData = beginOutputData(i); outputData; 
              outputData = nextOutputData(i)) {
            
            int n = outputData->accumulator[j]->count();
            if (n != 0) {
              writeStdDev( outStream, outputData, j );
            }
          }
          outStream << std::endl;
        }
      }
      
      outStream.flush();
      outStream.close();      
      
    } else {      
      sprintf(painCave.errMsg, "SpatialStatistics: unable to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }   
  }
  
  
  void SpatialStatistics::writeData(ostream& os, OutputData* dat, 
                                    unsigned int bin) {
    assert(int(bin) < nBins_);
    int n = dat->accumulator[bin]->count();
    if (n == 0) return;

    RealType r;
    Vector3d v;

    if( dat->dataType == odtReal ) {
      dynamic_cast<Accumulator*>(dat->accumulator[bin])->getAverage(r);      
      if (isinf(r) || isnan(r) ) {      
        sprintf( painCave.errMsg,
                 "SpatialStatistics detected a numerical error writing:\n"
                 "\t%s for bin %d",
                 dat->title.c_str(), bin);
        painCave.isFatal = 1;
        simError();
      }
      if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count();
      os << "\t" << r;      

    } else if ( dat->dataType == odtVector3 ) {
      dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getAverage(v);
      if (isinf(v[0]) || isnan(v[0]) || 
          isinf(v[1]) || isnan(v[1]) || 
          isinf(v[2]) || isnan(v[2]) ) {      
        sprintf( painCave.errMsg,
                 "SpatialStatistics detected a numerical error writing:\n"
                 "\t%s for bin %d",
                 dat->title.c_str(), bin);
        painCave.isFatal = 1;
        simError();
      }
      if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count();
      os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2];
    }
  }

  void SpatialStatistics::writeStdDev(ostream& os, OutputData* dat, 
                                    unsigned int bin) {
    assert(int(bin) < nBins_);
    int n = dat->accumulator[bin]->count();
    if (n == 0) return;

    RealType r;
    Vector3d v;

    if( dat->dataType == odtReal ) {
      dynamic_cast<Accumulator*>(dat->accumulator[bin])->getStdDev(r);      
      if (isinf(r) || isnan(r) ) {      
        sprintf( painCave.errMsg,
                 "SpatialStatistics detected a numerical error writing:\n"
                 "\tstandard deviation of %s for bin %d",
                 dat->title.c_str(), bin);
        painCave.isFatal = 1;
        simError();
      }
      if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count();
      os << "\t" << r;      

    } else if ( dat->dataType == odtVector3 ) {
      dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getStdDev(v);
      if (isinf(v[0]) || isnan(v[0]) || 
          isinf(v[1]) || isnan(v[1]) || 
          isinf(v[2]) || isnan(v[2]) ) {      
        sprintf( painCave.errMsg,
                 "SpatialStatistics detected a numerical error writing:\n"
                 "\tstandard deviation of %s for bin %d",
                 dat->title.c_str(), bin);
        painCave.isFatal = 1;
        simError();
      }
      if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count();
      os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2];
    }
  }
  
  
  OutputData* SpatialStatistics::beginOutputData(vector<OutputData*>::iterator& i) {
    i = data_.begin();
    return i != data_.end()? *i : NULL;
  }

  OutputData* SpatialStatistics::nextOutputData(vector<OutputData*>::iterator& i){
    ++i;
    return i != data_.end()? *i: NULL;
  }


  SlabStatistics::SlabStatistics(SimInfo* info, const string& filename, 
                                 const string& sele, int nbins) : 
    SpatialStatistics(info, filename, sele, nbins) {
    
    z_ = new OutputData;
    z_->units =  "Angstroms";
    z_->title =  "Z";
    z_->dataType = odtReal;
    z_->dataHandling = odhAverage;
    z_->accumulator.reserve(nbins);
    for (int i = 0; i < nbins; i++) 
      z_->accumulator.push_back( new Accumulator() );
    data_.push_back(z_);
  }

  void SlabStatistics::processFrame(int istep) {
    RealType z;
    hmat_ = currentSnapshot_->getHmat();
    for (int i = 0; i < nBins_; i++) {
      z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2);
      dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z);
    }
    volume_ = currentSnapshot_->getVolume();

    SpatialStatistics::processFrame(istep);
  }

  int SlabStatistics::getBin(Vector3d pos) {
    currentSnapshot_->wrapVector(pos);
    // which bin is this stuntdouble in?
    // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
    // Shift molecules by half a box to have bins start at 0
    // The modulo operator is used to wrap the case when we are 
    // beyond the end of the bins back to the beginning.
    return int(nBins_ * (pos.z() / hmat_(2,2) + 0.5)) % nBins_;  
  }


  ShellStatistics::ShellStatistics(SimInfo* info, const string& filename, 
                                   const string& sele, int nbins) : 
    SpatialStatistics(info, filename, sele, nbins){
    
    coordinateOrigin_ = V3Zero;
    binWidth_ = 1.0;

    r_ = new OutputData;
    r_->units =  "Angstroms";
    r_->title =  "R";
    r_->dataType = odtReal;
    r_->dataHandling = odhAverage;
    r_->accumulator.reserve(nbins);
    for (int i = 0; i < nbins; i++)
      r_->accumulator.push_back( new Accumulator() );    
    data_.push_back(r_);

    for (int i = 0; i < nbins; i++) {
      RealType r = (((RealType)i + 0.5) * binWidth_);
      dynamic_cast<Accumulator*>(r_->accumulator[i])->add(r);
    }
  }

  int ShellStatistics::getBin(Vector3d pos) {    
    Vector3d rPos = pos - coordinateOrigin_;
    return int(rPos.length() / binWidth_);
  }
}

Revision:	1865
Committed:	Wed Apr 17 18:24:08 2013 UTC (12 years ago) by gezelter
Original Path:	*branches/development/src/applications/staticProps/SpatialStatistics.cpp*
File size:	12478 byte(s)
Log Message:	Adding spatial statistics analysers.
#	User	Rev	Content
1	gezelter	1865	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* 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			*
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, 234107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include "applications/staticProps/SpatialStatistics.hpp"
44			#include "io/DumpReader.hpp"
45			#include "primitives/Molecule.hpp"
46
47			namespace OpenMD {
48
49			SpatialStatistics::SpatialStatistics(SimInfo* info, const string& filename,
50			const string& sele, int nbins)
51			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info),
52			seleMan_(info), nBins_(nbins){
53
54			evaluator_.loadScriptString(sele);
55			if (!evaluator_.isDynamic()) {
56			seleMan_.setSelectionSet(evaluator_.evaluate());
57			}
58
59			// Pre-load an OutputData for the count of objects:
60			counts_ = new OutputData;
61			counts_->units = "objects";
62			counts_->title = "Objects";
63			counts_->dataType = odtReal;
64			counts_->dataHandling = odhTotal;
65			counts_->accumulator.reserve(nBins_);
66			for (int i = 0; i < nBins_; i++)
67			counts_->accumulator.push_back( new Accumulator() );
68
69			setOutputName(getPrefix(filename) + ".spst");
70			}
71
72			SpatialStatistics::~SpatialStatistics() {
73			vector<OutputData*>::iterator i;
74			OutputData* outputData;
75
76			for(outputData = beginOutputData(i); outputData;
77			outputData = nextOutputData(i)) {
78			delete outputData;
79			}
80			data_.clear();
81
82			delete counts_;
83			}
84
85
86			void SpatialStatistics::process() {
87
88			DumpReader reader(info_, dumpFilename_);
89			int nFrames = reader.getNFrames();
90			nProcessed_ = nFrames/step_;
91
92			for (int istep = 0; istep < nFrames; istep += step_) {
93			reader.readFrame(istep);
94			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
95			processFrame(istep);
96			}
97			writeOutput();
98			}
99
100
101			void SpatialStatistics::processFrame(int istep) {
102			Molecule* mol;
103			RigidBody* rb;
104			StuntDouble* sd;
105			SimInfo::MoleculeIterator mi;
106			Molecule::RigidBodyIterator rbIter;
107			int i;
108
109			for (mol = info_->beginMolecule(mi); mol != NULL;
110			mol = info_->nextMolecule(mi)) {
111
112			// change the positions of atoms which belong to the rigidbodies
113
114			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
115			rb = mol->nextRigidBody(rbIter)) {
116			rb->updateAtoms();
117			}
118			}
119
120			if (evaluator_.isDynamic()) {
121			seleMan_.setSelectionSet(evaluator_.evaluate());
122			}
123
124			// loop over the selected atoms:
125
126			for (sd = seleMan_.beginSelected(i); sd != NULL;
127			sd = seleMan_.nextSelected(i)) {
128
129			// figure out where that object is:
130
131			Vector3d pos = sd->getPos();
132
133			int bin = getBin(pos);
134
135			// forward the work of statistics on to the subclass:
136
137			processStuntDouble( sd, bin );
138
139			dynamic_cast<Accumulator *>(counts_->accumulator[bin])->add(1);
140			}
141			}
142
143
144			void SpatialStatistics::writeOutput() {
145
146			vector<OutputData*>::iterator i;
147			OutputData* outputData;
148
149			ofstream outStream(outputFilename_.c_str());
150			if (outStream.is_open()) {
151
152			//write title
153			outStream << "# SPATIAL STATISTICS\n";
154			outStream << "#";
155
156			for(outputData = beginOutputData(i); outputData;
157			outputData = nextOutputData(i)) {
158			outStream << "\t" << outputData->title <<
159			"(" << outputData->units << ")";
160			// add some extra tabs for column alignment
161			if (outputData->dataType == odtVector3) outStream << "\t\t";
162			}
163
164			outStream << std::endl;
165
166			outStream.precision(8);
167
168			for (int j = 0; j < nBins_; j++) {
169
170			int counts = counts_->accumulator[j]->count();
171
172			if (counts > 0) {
173			for(outputData = beginOutputData(i); outputData;
174			outputData = nextOutputData(i)) {
175
176			int n = outputData->accumulator[j]->count();
177			if (n != 0) {
178			writeData( outStream, outputData, j );
179			}
180			}
181			outStream << std::endl;
182			}
183			}
184
185			outStream << "#######################################################\n";
186			outStream << "# Standard Deviations in those quantities follow:\n";
187			outStream << "#######################################################\n";
188
189			for (int j = 0; j < nBins_; j++) {
190			int counts = counts_->accumulator[j]->count();
191			if (counts > 0) {
192
193			outStream << "#";
194			for(outputData = beginOutputData(i); outputData;
195			outputData = nextOutputData(i)) {
196
197			int n = outputData->accumulator[j]->count();
198			if (n != 0) {
199			writeStdDev( outStream, outputData, j );
200			}
201			}
202			outStream << std::endl;
203			}
204			}
205
206			outStream.flush();
207			outStream.close();
208
209			} else {
210			sprintf(painCave.errMsg, "SpatialStatistics: unable to open %s\n",
211			outputFilename_.c_str());
212			painCave.isFatal = 1;
213			simError();
214			}
215			}
216
217
218			void SpatialStatistics::writeData(ostream& os, OutputData* dat,
219			unsigned int bin) {
220			assert(int(bin) < nBins_);
221			int n = dat->accumulator[bin]->count();
222			if (n == 0) return;
223
224			RealType r;
225			Vector3d v;
226
227			if( dat->dataType == odtReal ) {
228			dynamic_cast<Accumulator*>(dat->accumulator[bin])->getAverage(r);
229			if (isinf(r) \|\| isnan(r) ) {
230			sprintf( painCave.errMsg,
231			"SpatialStatistics detected a numerical error writing:\n"
232			"\t%s for bin %d",
233			dat->title.c_str(), bin);
234			painCave.isFatal = 1;
235			simError();
236			}
237			if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count();
238			os << "\t" << r;
239
240			} else if ( dat->dataType == odtVector3 ) {
241			dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getAverage(v);
242			if (isinf(v[0]) \|\| isnan(v[0]) \|\|
243			isinf(v[1]) \|\| isnan(v[1]) \|\|
244			isinf(v[2]) \|\| isnan(v[2]) ) {
245			sprintf( painCave.errMsg,
246			"SpatialStatistics detected a numerical error writing:\n"
247			"\t%s for bin %d",
248			dat->title.c_str(), bin);
249			painCave.isFatal = 1;
250			simError();
251			}
252			if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count();
253			os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2];
254			}
255			}
256
257			void SpatialStatistics::writeStdDev(ostream& os, OutputData* dat,
258			unsigned int bin) {
259			assert(int(bin) < nBins_);
260			int n = dat->accumulator[bin]->count();
261			if (n == 0) return;
262
263			RealType r;
264			Vector3d v;
265
266			if( dat->dataType == odtReal ) {
267			dynamic_cast<Accumulator*>(dat->accumulator[bin])->getStdDev(r);
268			if (isinf(r) \|\| isnan(r) ) {
269			sprintf( painCave.errMsg,
270			"SpatialStatistics detected a numerical error writing:\n"
271			"\tstandard deviation of %s for bin %d",
272			dat->title.c_str(), bin);
273			painCave.isFatal = 1;
274			simError();
275			}
276			if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count();
277			os << "\t" << r;
278
279			} else if ( dat->dataType == odtVector3 ) {
280			dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getStdDev(v);
281			if (isinf(v[0]) \|\| isnan(v[0]) \|\|
282			isinf(v[1]) \|\| isnan(v[1]) \|\|
283			isinf(v[2]) \|\| isnan(v[2]) ) {
284			sprintf( painCave.errMsg,
285			"SpatialStatistics detected a numerical error writing:\n"
286			"\tstandard deviation of %s for bin %d",
287			dat->title.c_str(), bin);
288			painCave.isFatal = 1;
289			simError();
290			}
291			if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count();
292			os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2];
293			}
294			}
295
296
297			OutputData* SpatialStatistics::beginOutputData(vector<OutputData*>::iterator& i) {
298			i = data_.begin();
299			return i != data_.end()? *i : NULL;
300			}
301
302			OutputData* SpatialStatistics::nextOutputData(vector<OutputData*>::iterator& i){
303			++i;
304			return i != data_.end()? *i: NULL;
305			}
306
307
308			SlabStatistics::SlabStatistics(SimInfo* info, const string& filename,
309			const string& sele, int nbins) :
310			SpatialStatistics(info, filename, sele, nbins) {
311
312			z_ = new OutputData;
313			z_->units = "Angstroms";
314			z_->title = "Z";
315			z_->dataType = odtReal;
316			z_->dataHandling = odhAverage;
317			z_->accumulator.reserve(nbins);
318			for (int i = 0; i < nbins; i++)
319			z_->accumulator.push_back( new Accumulator() );
320			data_.push_back(z_);
321			}
322
323			void SlabStatistics::processFrame(int istep) {
324			RealType z;
325			hmat_ = currentSnapshot_->getHmat();
326			for (int i = 0; i < nBins_; i++) {
327			z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2);
328			dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z);
329			}
330			volume_ = currentSnapshot_->getVolume();
331
332			SpatialStatistics::processFrame(istep);
333			}
334
335			int SlabStatistics::getBin(Vector3d pos) {
336			currentSnapshot_->wrapVector(pos);
337			// which bin is this stuntdouble in?
338			// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
339			// Shift molecules by half a box to have bins start at 0
340			// The modulo operator is used to wrap the case when we are
341			// beyond the end of the bins back to the beginning.
342			return int(nBins_ * (pos.z() / hmat_(2,2) + 0.5)) % nBins_;
343			}
344
345
346			ShellStatistics::ShellStatistics(SimInfo* info, const string& filename,
347			const string& sele, int nbins) :
348			SpatialStatistics(info, filename, sele, nbins){
349
350			coordinateOrigin_ = V3Zero;
351			binWidth_ = 1.0;
352
353			r_ = new OutputData;
354			r_->units = "Angstroms";
355			r_->title = "R";
356			r_->dataType = odtReal;
357			r_->dataHandling = odhAverage;
358			r_->accumulator.reserve(nbins);
359			for (int i = 0; i < nbins; i++)
360			r_->accumulator.push_back( new Accumulator() );
361			data_.push_back(r_);
362
363			for (int i = 0; i < nbins; i++) {
364			RealType r = (((RealType)i + 0.5) * binWidth_);
365			dynamic_cast<Accumulator*>(r_->accumulator[i])->add(r);
366			}
367			}
368
369			int ShellStatistics::getBin(Vector3d pos) {
370			Vector3d rPos = pos - coordinateOrigin_;
371			return int(rPos.length() / binWidth_);
372			}
373			}
374