applications/staticProps/RNEMDStats.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).
 */


#include <algorithm>
#include <fstream>
#include "applications/staticProps/RNEMDStats.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {
  
  RNEMDZ::RNEMDZ(SimInfo* info, const std::string& filename, 
                 const std::string& sele, int nzbins)
    : SlabStatistics(info, filename, sele, nzbins) {
        
    setOutputName(getPrefix(filename) + ".rnemdZ");
    
    temperature = new OutputData;
    temperature->units =  "K";
    temperature->title =  "Temperature";
    temperature->dataType = odtReal;
    temperature->dataHandling = odhAverage;
    temperature->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      temperature->accumulator.push_back( new Accumulator() );
    data_.push_back(temperature);
    
    velocity = new OutputData;
    velocity->units = "angstroms/fs";
    velocity->title =  "Velocity";  
    velocity->dataType = odtVector3;
    velocity->dataHandling = odhAverage;
    velocity->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      velocity->accumulator.push_back( new VectorAccumulator() );
    data_.push_back(velocity);
    
    density = new OutputData;
    density->units =  "g cm^-3";
    density->title =  "Density";
    density->dataType = odtReal;
    density->dataHandling = odhAverage;
    density->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      density->accumulator.push_back( new Accumulator() );
    data_.push_back(density);
  }

  void RNEMDZ::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();


    Molecule* mol;
    RigidBody* rb;
    StuntDouble* sd;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    int i;

    vector<RealType> binMass(nBins_, 0.0);
    vector<RealType> binPx(nBins_, 0.0);
    vector<RealType> binPy(nBins_, 0.0);
    vector<RealType> binPz(nBins_, 0.0);
    vector<RealType> binKE(nBins_, 0.0);
    vector<unsigned int> binDof(nBins_, 0);
    vector<unsigned int> binCount(nBins_, 0);
    
    
    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->updateAtomVel();
      }
    }
   
    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(); 
      Vector3d vel = sd->getVel();
      RealType m = sd->getMass();

      int bin = getBin(pos);

      binCount[bin] += 1;

      binMass[bin] += m;
      binPx[bin] += m * vel.x();
      binPy[bin] += m * vel.y();
      binPz[bin] += m * vel.z();
      binKE[bin] += 0.5 * (m * vel.lengthSquare());
      binDof[bin] += 3;
      
      if (sd->isDirectional()) {
        Vector3d angMom = sd->getJ();
        Mat3x3d I = sd->getI();
        if (sd->isLinear()) {
          int i = sd->linearAxis();
          int j = (i + 1) % 3;
          int k = (i + 2) % 3;
          binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) + 
                               angMom[k] * angMom[k] / I(k, k));
          binDof[bin] += 2;
        } else {
          binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
                               angMom[1] * angMom[1] / I(1, 1) +
                               angMom[2] * angMom[2] / I(2, 2));
          binDof[bin] += 3;
        }
      }
    }
    
    for (unsigned int i = 0; i < nBins_; i++) {

      if (binDof[i] > 0) {
        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
                                          PhysicalConstants::energyConvert);
        RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert 
          / volume_;
        Vector3d vel;
        vel.x() = binPx[i] / binMass[i];
        vel.y() = binPy[i] / binMass[i];
        vel.z() = binPz[i] / binMass[i];

        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
        dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel);
        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
      }
    }
  }
  
  void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
  }

  RNEMDR::RNEMDR(SimInfo* info, const std::string& filename, 
                 const std::string& sele, int nrbins)
    : ShellStatistics(info, filename, sele, nrbins) {
        

    setOutputName(getPrefix(filename) + ".rnemdR");
    
    temperature = new OutputData;
    temperature->units =  "K";
    temperature->title =  "Temperature";
    temperature->dataType = odtReal;
    temperature->dataHandling = odhAverage;
    temperature->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      temperature->accumulator.push_back( new Accumulator() );
    data_.push_back(temperature);
    
    angularVelocity = new OutputData;
    angularVelocity->units = "angstroms^2/fs";
    angularVelocity->title =  "Velocity";  
    angularVelocity->dataType = odtVector3;
    angularVelocity->dataHandling = odhAverage;
    angularVelocity->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      angularVelocity->accumulator.push_back( new VectorAccumulator() );
    data_.push_back(angularVelocity);
    
    density = new OutputData;
    density->units =  "g cm^-3";
    density->title =  "Density";
    density->dataType = odtReal;
    density->dataHandling = odhAverage;
    density->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      density->accumulator.push_back( new Accumulator() );
    data_.push_back(density);
  }


  void RNEMDR::processFrame(int istep) {

    Molecule* mol;
    RigidBody* rb;
    StuntDouble* sd;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    int i;

    vector<RealType> binMass(nBins_, 0.0);
    vector<Vector3d> binaVel(nBins_, V3Zero);
    vector<RealType> binKE(nBins_, 0.0);
    vector<unsigned int> binDof(nBins_, 0);
    vector<unsigned int> binCount(nBins_, 0);
    
    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->updateAtomVel();
      }
    }
   
    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 rPos = sd->getPos() - coordinateOrigin_;
      Vector3d vel = sd->getVel();      
      Vector3d aVel = cross(rPos, vel);
      RealType m = sd->getMass();

      int bin = getBin(rPos);

      binCount[bin] += 1;

      binMass[bin] += m;
      binaVel[bin] += aVel;
      binKE[bin] += 0.5 * (m * vel.lengthSquare());
      binDof[bin] += 3;
      
      if (sd->isDirectional()) {
        Vector3d angMom = sd->getJ();
        Mat3x3d I = sd->getI();
        if (sd->isLinear()) {
          int i = sd->linearAxis();
          int j = (i + 1) % 3;
          int k = (i + 2) % 3;
          binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) + 
                               angMom[k] * angMom[k] / I(k, k));
          binDof[bin] += 2;
        } else {
          binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
                               angMom[1] * angMom[1] / I(1, 1) +
                               angMom[2] * angMom[2] / I(2, 2));
          binDof[bin] += 3;
        }
      }
    }
    
    for (unsigned int i = 0; i < nBins_; i++) {
      RealType rinner = (RealType)i * binWidth_;
      RealType router = (RealType)(i+1) * binWidth_;
      if (binDof[i] > 0) {
        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
                                          PhysicalConstants::energyConvert);
        RealType den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
          / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));  
        Vector3d aVel = binaVel[i] / RealType(binCount[i]);
        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
        dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(aVel);
        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
      }
    }
  }


  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
  }
}

Revision:	1892
Committed:	Wed Jun 19 14:14:56 2013 UTC (11 years, 10 months ago) by gezelter
File size:	11257 byte(s)
Log Message:	Made RNEMD stats exactly the same as in the RNEMD module.
#	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			*/
41
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/RNEMDStats.hpp"
46	gezelter	1881	#include "primitives/Molecule.hpp"
47	gezelter	1865	#include "utils/PhysicalConstants.hpp"
48
49			namespace OpenMD {
50
51			RNEMDZ::RNEMDZ(SimInfo* info, const std::string& filename,
52			const std::string& sele, int nzbins)
53			: SlabStatistics(info, filename, sele, nzbins) {
54
55			setOutputName(getPrefix(filename) + ".rnemdZ");
56
57			temperature = new OutputData;
58			temperature->units = "K";
59			temperature->title = "Temperature";
60			temperature->dataType = odtReal;
61			temperature->dataHandling = odhAverage;
62			temperature->accumulator.reserve(nBins_);
63			for (int i = 0; i < nBins_; i++)
64			temperature->accumulator.push_back( new Accumulator() );
65			data_.push_back(temperature);
66
67			velocity = new OutputData;
68			velocity->units = "angstroms/fs";
69			velocity->title = "Velocity";
70			velocity->dataType = odtVector3;
71			velocity->dataHandling = odhAverage;
72			velocity->accumulator.reserve(nBins_);
73			for (int i = 0; i < nBins_; i++)
74			velocity->accumulator.push_back( new VectorAccumulator() );
75			data_.push_back(velocity);
76
77			density = new OutputData;
78			density->units = "g cm^-3";
79			density->title = "Density";
80			density->dataType = odtReal;
81			density->dataHandling = odhAverage;
82			density->accumulator.reserve(nBins_);
83			for (int i = 0; i < nBins_; i++)
84			density->accumulator.push_back( new Accumulator() );
85			data_.push_back(density);
86			}
87
88	gezelter	1881	void RNEMDZ::processFrame(int istep) {
89	gezelter	1884	RealType z;
90
91			hmat_ = currentSnapshot_->getHmat();
92			for (int i = 0; i < nBins_; i++) {
93			z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2);
94			dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z);
95			}
96			volume_ = currentSnapshot_->getVolume();
97
98
99	gezelter	1881	Molecule* mol;
100			RigidBody* rb;
101			StuntDouble* sd;
102			SimInfo::MoleculeIterator mi;
103			Molecule::RigidBodyIterator rbIter;
104			int i;
105	gezelter	1865
106	gezelter	1881	vector<RealType> binMass(nBins_, 0.0);
107	gezelter	1892	vector<RealType> binPx(nBins_, 0.0);
108			vector<RealType> binPy(nBins_, 0.0);
109			vector<RealType> binPz(nBins_, 0.0);
110	gezelter	1881	vector<RealType> binKE(nBins_, 0.0);
111	gezelter	1883	vector<unsigned int> binDof(nBins_, 0);
112			vector<unsigned int> binCount(nBins_, 0);
113	gezelter	1881
114
115			for (mol = info_->beginMolecule(mi); mol != NULL;
116			mol = info_->nextMolecule(mi)) {
117
118			// change the positions of atoms which belong to the rigidbodies
119
120			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
121			rb = mol->nextRigidBody(rbIter)) {
122	gezelter	1892	rb->updateAtomVel();
123	gezelter	1865	}
124			}
125	gezelter	1884
126	gezelter	1881	if (evaluator_.isDynamic()) {
127			seleMan_.setSelectionSet(evaluator_.evaluate());
128			}
129	gezelter	1865
130	gezelter	1881	// loop over the selected atoms:
131
132			for (sd = seleMan_.beginSelected(i); sd != NULL;
133			sd = seleMan_.nextSelected(i)) {
134
135			// figure out where that object is:
136			Vector3d pos = sd->getPos();
137	gezelter	1883	Vector3d vel = sd->getVel();
138			RealType m = sd->getMass();
139
140	gezelter	1881	int bin = getBin(pos);
141	gezelter	1884
142	gezelter	1883	binCount[bin] += 1;
143	gezelter	1881
144			binMass[bin] += m;
145	gezelter	1892	binPx[bin] += m * vel.x();
146			binPy[bin] += m * vel.y();
147			binPz[bin] += m * vel.z();
148	gezelter	1881	binKE[bin] += 0.5 * (m * vel.lengthSquare());
149			binDof[bin] += 3;
150
151			if (sd->isDirectional()) {
152			Vector3d angMom = sd->getJ();
153			Mat3x3d I = sd->getI();
154			if (sd->isLinear()) {
155			int i = sd->linearAxis();
156			int j = (i + 1) % 3;
157			int k = (i + 2) % 3;
158			binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
159			angMom[k] * angMom[k] / I(k, k));
160			binDof[bin] += 2;
161			} else {
162			binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
163			angMom[1] * angMom[1] / I(1, 1) +
164			angMom[2] * angMom[2] / I(2, 2));
165			binDof[bin] += 3;
166			}
167			}
168			}
169
170	gezelter	1883	for (unsigned int i = 0; i < nBins_; i++) {
171	gezelter	1885
172	gezelter	1882	if (binDof[i] > 0) {
173			RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
174			PhysicalConstants::energyConvert);
175			RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
176			/ volume_;
177	gezelter	1892	Vector3d vel;
178			vel.x() = binPx[i] / binMass[i];
179			vel.y() = binPy[i] / binMass[i];
180			vel.z() = binPz[i] / binMass[i];
181
182	gezelter	1882	dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
183			dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel);
184			dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
185			dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
186			}
187	gezelter	1881	}
188	gezelter	1865	}
189	gezelter	1881
190			void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
191			}
192	gezelter	1865
193			RNEMDR::RNEMDR(SimInfo* info, const std::string& filename,
194			const std::string& sele, int nrbins)
195			: ShellStatistics(info, filename, sele, nrbins) {
196
197
198			setOutputName(getPrefix(filename) + ".rnemdR");
199
200			temperature = new OutputData;
201			temperature->units = "K";
202			temperature->title = "Temperature";
203			temperature->dataType = odtReal;
204			temperature->dataHandling = odhAverage;
205			temperature->accumulator.reserve(nBins_);
206			for (int i = 0; i < nBins_; i++)
207			temperature->accumulator.push_back( new Accumulator() );
208			data_.push_back(temperature);
209
210			angularVelocity = new OutputData;
211			angularVelocity->units = "angstroms^2/fs";
212			angularVelocity->title = "Velocity";
213			angularVelocity->dataType = odtVector3;
214			angularVelocity->dataHandling = odhAverage;
215			angularVelocity->accumulator.reserve(nBins_);
216			for (int i = 0; i < nBins_; i++)
217			angularVelocity->accumulator.push_back( new VectorAccumulator() );
218			data_.push_back(angularVelocity);
219
220			density = new OutputData;
221			density->units = "g cm^-3";
222			density->title = "Density";
223			density->dataType = odtReal;
224			density->dataHandling = odhAverage;
225			density->accumulator.reserve(nBins_);
226			for (int i = 0; i < nBins_; i++)
227			density->accumulator.push_back( new Accumulator() );
228			data_.push_back(density);
229			}
230
231
232	gezelter	1887	void RNEMDR::processFrame(int istep) {
233	gezelter	1865
234	gezelter	1887	Molecule* mol;
235			RigidBody* rb;
236			StuntDouble* sd;
237			SimInfo::MoleculeIterator mi;
238			Molecule::RigidBodyIterator rbIter;
239			int i;
240
241			vector<RealType> binMass(nBins_, 0.0);
242			vector<Vector3d> binaVel(nBins_, V3Zero);
243			vector<RealType> binKE(nBins_, 0.0);
244			vector<unsigned int> binDof(nBins_, 0);
245			vector<unsigned int> binCount(nBins_, 0);
246
247			for (mol = info_->beginMolecule(mi); mol != NULL;
248			mol = info_->nextMolecule(mi)) {
249
250			// change the positions of atoms which belong to the rigidbodies
251
252			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
253			rb = mol->nextRigidBody(rbIter)) {
254	gezelter	1892	rb->updateAtomVel();
255	gezelter	1865	}
256			}
257	gezelter	1887
258			if (evaluator_.isDynamic()) {
259			seleMan_.setSelectionSet(evaluator_.evaluate());
260			}
261	gezelter	1865
262	gezelter	1887	// loop over the selected atoms:
263
264			for (sd = seleMan_.beginSelected(i); sd != NULL;
265			sd = seleMan_.nextSelected(i)) {
266
267			// figure out where that object is:
268	gezelter	1865
269	gezelter	1887	Vector3d rPos = sd->getPos() - coordinateOrigin_;
270			Vector3d vel = sd->getVel();
271			Vector3d aVel = cross(rPos, vel);
272			RealType m = sd->getMass();
273
274	gezelter	1888	int bin = getBin(rPos);
275	gezelter	1887
276			binCount[bin] += 1;
277
278			binMass[bin] += m;
279			binaVel[bin] += aVel;
280			binKE[bin] += 0.5 * (m * vel.lengthSquare());
281			binDof[bin] += 3;
282
283			if (sd->isDirectional()) {
284			Vector3d angMom = sd->getJ();
285			Mat3x3d I = sd->getI();
286			if (sd->isLinear()) {
287			int i = sd->linearAxis();
288			int j = (i + 1) % 3;
289			int k = (i + 2) % 3;
290			binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
291			angMom[k] * angMom[k] / I(k, k));
292			binDof[bin] += 2;
293			} else {
294			binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
295			angMom[1] * angMom[1] / I(1, 1) +
296			angMom[2] * angMom[2] / I(2, 2));
297			binDof[bin] += 3;
298			}
299			}
300			}
301	gezelter	1865
302	gezelter	1887	for (unsigned int i = 0; i < nBins_; i++) {
303			RealType rinner = (RealType)i * binWidth_;
304			RealType router = (RealType)(i+1) * binWidth_;
305			if (binDof[i] > 0) {
306			RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
307			PhysicalConstants::energyConvert);
308			RealType den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
309			/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
310			Vector3d aVel = binaVel[i] / RealType(binCount[i]);
311			dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
312			dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(aVel);
313			dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
314			dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
315			}
316			}
317			}
318	gezelter	1865
319	gezelter	1887
320			void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
321	gezelter	1865	}
322			}
323