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<Vector3d> binP(nBins_, V3Zero);
    vector<RealType> binKE(nBins_, 0.0);
    vector<unsigned int> binDof(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);

      binMass[bin] += m;
      binP[bin] += m * vel;
      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 (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 = binP[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 =  "Angular 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<Mat3x3d>  binI(nBins_);
    vector<Vector3d> binL(nBins_, V3Zero);
    vector<RealType> binKE(nBins_, 0.0);
    vector<int> binDof(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:
      int bin = getBin( sd->getPos() );   

      if (bin >= 0 && bin < nBins_)  {

        Vector3d rPos = sd->getPos() - coordinateOrigin_;
        Vector3d vel = sd->getVel();      
        RealType m = sd->getMass();
        Vector3d L = m * cross(rPos, vel);
        Mat3x3d I(0.0);
        I = outProduct(rPos, rPos) * m;
        RealType r2 = rPos.lengthSquare();
        I(0, 0) += m * r2;
        I(1, 1) += m * r2;
        I(2, 2) += m * r2;       

        binMass[bin] += m;
        binI[bin] += I;
        binL[bin] += L;
        binKE[bin] += 0.5 * (m * vel.lengthSquare());
        binDof[bin] += 3;
        
        if (sd->isDirectional()) {
          Vector3d angMom = sd->getJ();
          Mat3x3d Ia = 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] / Ia(j, j) + 
                                 angMom[k] * angMom[k] / Ia(k, k));
            binDof[bin] += 2;
          } else {
            binKE[bin] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
                                 angMom[1] * angMom[1] / Ia(1, 1) +
                                 angMom[2] * angMom[2] / Ia(2, 2));
            binDof[bin] += 3;
          }
        }
      }
    }
    
    for (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 omega = binI[i].inverse() * binL[i];
 
        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
        dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(omega);
        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
      }
    }
  }


  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
  }
  
  RNEMDRTheta::RNEMDRTheta(SimInfo* info, const std::string& filename, 
                           const std::string& sele, int nrbins, int nangleBins)
    : ShellStatistics(info, filename, sele, nrbins), nAngleBins_(nangleBins) {
    
    Globals* simParams = info->getSimParams();
    RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
    bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
    
    if (hasAngularMomentumFluxVector) {
      fluxVector_ = rnemdParams->getAngularMomentumFluxVector();
    } else {
      
      std::string fluxStr = rnemdParams->getFluxType();
      if (fluxStr.find("Lx") != std::string::npos) {
        fluxVector_ = V3X;
      } else if (fluxStr.find("Ly") != std::string::npos) {
        fluxVector_ = V3Y;
      } else {
        fluxVector_ = V3Z;
      }
    }
    
    fluxVector_.normalize();

    setOutputName(getPrefix(filename) + ".rnemdRTheta");

    angularVelocity = new OutputData;
    angularVelocity->units = "angstroms^2/fs";
    angularVelocity->title =  "Angular Velocity";  
    angularVelocity->dataType = odtArray2d;
    angularVelocity->dataHandling = odhAverage;
    angularVelocity->accumulatorArray2d.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) {
      angularVelocity->accumulatorArray2d[i].reserve(nAngleBins_);
      for (int j = 0 ; j < nAngleBins_; j++) {       
        angularVelocity->accumulatorArray2d[i][j] = new Accumulator();
      }
    }
    data_.push_back(angularVelocity);

  }


  std::pair<int,int> RNEMDRTheta::getBins(Vector3d pos) { 
    std::pair<int,int> result;

    Vector3d rPos = pos - coordinateOrigin_;
    RealType cosAngle= dot(rPos, fluxVector_) / rPos.length();

    result.first = int(rPos.length() / binWidth_);
    result.second = int( (nAngleBins_ - 1) * 0.5 * (cosAngle + 1.0) );
    return result;
  }

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

  void RNEMDRTheta::processFrame(int istep) {

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

    vector<vector<Mat3x3d> >  binI;
    vector<vector<Vector3d> > binL;
    vector<vector<int> > binCount;
    
    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:
      std::pair<int,int> bins = getBins( sd->getPos() );   

      if (bins.first >= 0 && bins.first < nBins_)  {
        if (bins.second >= 0 && bins.second < nAngleBins_) {

          Vector3d rPos = sd->getPos() - coordinateOrigin_;
          Vector3d vel = sd->getVel();      
          RealType m = sd->getMass();
          Vector3d L = m * cross(rPos, vel);
          Mat3x3d I(0.0);
          I = outProduct(rPos, rPos) * m;
          RealType r2 = rPos.lengthSquare();
          I(0, 0) += m * r2;
          I(1, 1) += m * r2;
          I(2, 2) += m * r2;       

          binI[bins.first][bins.second] += I;
          binL[bins.first][bins.second] += L;
          binCount[bins.first][bins.second]++;
        }
      }
    }
  
    
    for (int i = 0; i < nBins_; i++) {
      for (int j = 0; j < nAngleBins_; j++) {

        if (binCount[i][j] > 0) {
          Vector3d omega = binI[i][j].inverse() * binL[i][j];
          RealType omegaProj = dot(omega, fluxVector_);
 
          dynamic_cast<Accumulator *>(angularVelocity->accumulatorArray2d[i][j])->add(omegaProj);
        }
      }
    }
  }

  void RNEMDRTheta::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;
        }
      }
    }
  }
}

Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 5 months ago) by gezelter
File size:	16338 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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	1944	vector<Vector3d> binP(nBins_, V3Zero);
108	gezelter	1881	vector<RealType> binKE(nBins_, 0.0);
109	gezelter	1883	vector<unsigned int> binDof(nBins_, 0);
110	gezelter	1881
111			for (mol = info_->beginMolecule(mi); mol != NULL;
112			mol = info_->nextMolecule(mi)) {
113
114			// change the positions of atoms which belong to the rigidbodies
115
116			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
117			rb = mol->nextRigidBody(rbIter)) {
118	gezelter	1892	rb->updateAtomVel();
119	gezelter	1865	}
120			}
121	gezelter	1884
122	gezelter	1881	if (evaluator_.isDynamic()) {
123			seleMan_.setSelectionSet(evaluator_.evaluate());
124			}
125	gezelter	1865
126	gezelter	1881	// loop over the selected atoms:
127
128			for (sd = seleMan_.beginSelected(i); sd != NULL;
129			sd = seleMan_.nextSelected(i)) {
130
131			// figure out where that object is:
132			Vector3d pos = sd->getPos();
133	gezelter	1883	Vector3d vel = sd->getVel();
134			RealType m = sd->getMass();
135
136	gezelter	1881	int bin = getBin(pos);
137	gezelter	1884
138	gezelter	1881	binMass[bin] += m;
139	gezelter	1944	binP[bin] += m * vel;
140	gezelter	1881	binKE[bin] += 0.5 * (m * vel.lengthSquare());
141			binDof[bin] += 3;
142
143			if (sd->isDirectional()) {
144			Vector3d angMom = sd->getJ();
145			Mat3x3d I = sd->getI();
146			if (sd->isLinear()) {
147			int i = sd->linearAxis();
148			int j = (i + 1) % 3;
149			int k = (i + 2) % 3;
150			binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
151			angMom[k] * angMom[k] / I(k, k));
152			binDof[bin] += 2;
153			} else {
154			binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
155			angMom[1] * angMom[1] / I(1, 1) +
156			angMom[2] * angMom[2] / I(2, 2));
157			binDof[bin] += 3;
158			}
159			}
160			}
161
162	gezelter	1953	for (int i = 0; i < nBins_; i++) {
163	gezelter	1885
164	gezelter	1882	if (binDof[i] > 0) {
165			RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
166			PhysicalConstants::energyConvert);
167			RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
168			/ volume_;
169	gezelter	1944	Vector3d vel = binP[i] / binMass[i];
170	gezelter	1892
171	gezelter	1882	dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
172			dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel);
173			dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
174			dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
175			}
176	gezelter	1881	}
177	gezelter	1865	}
178	gezelter	1881
179			void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
180			}
181	gezelter	1865
182			RNEMDR::RNEMDR(SimInfo* info, const std::string& filename,
183			const std::string& sele, int nrbins)
184			: ShellStatistics(info, filename, sele, nrbins) {
185
186
187			setOutputName(getPrefix(filename) + ".rnemdR");
188
189			temperature = new OutputData;
190			temperature->units = "K";
191			temperature->title = "Temperature";
192			temperature->dataType = odtReal;
193			temperature->dataHandling = odhAverage;
194			temperature->accumulator.reserve(nBins_);
195			for (int i = 0; i < nBins_; i++)
196			temperature->accumulator.push_back( new Accumulator() );
197			data_.push_back(temperature);
198
199			angularVelocity = new OutputData;
200			angularVelocity->units = "angstroms^2/fs";
201	gezelter	1953	angularVelocity->title = "Angular Velocity";
202	gezelter	1865	angularVelocity->dataType = odtVector3;
203			angularVelocity->dataHandling = odhAverage;
204			angularVelocity->accumulator.reserve(nBins_);
205			for (int i = 0; i < nBins_; i++)
206			angularVelocity->accumulator.push_back( new VectorAccumulator() );
207			data_.push_back(angularVelocity);
208
209			density = new OutputData;
210			density->units = "g cm^-3";
211			density->title = "Density";
212			density->dataType = odtReal;
213			density->dataHandling = odhAverage;
214			density->accumulator.reserve(nBins_);
215			for (int i = 0; i < nBins_; i++)
216			density->accumulator.push_back( new Accumulator() );
217			data_.push_back(density);
218			}
219
220
221	gezelter	1887	void RNEMDR::processFrame(int istep) {
222	gezelter	1865
223	gezelter	1887	Molecule* mol;
224			RigidBody* rb;
225			StuntDouble* sd;
226			SimInfo::MoleculeIterator mi;
227			Molecule::RigidBodyIterator rbIter;
228			int i;
229
230			vector<RealType> binMass(nBins_, 0.0);
231	gezelter	1944	vector<Mat3x3d> binI(nBins_);
232			vector<Vector3d> binL(nBins_, V3Zero);
233	gezelter	1887	vector<RealType> binKE(nBins_, 0.0);
234	gezelter	1944	vector<int> binDof(nBins_, 0);
235	gezelter	1887
236			for (mol = info_->beginMolecule(mi); mol != NULL;
237			mol = info_->nextMolecule(mi)) {
238
239			// change the positions of atoms which belong to the rigidbodies
240
241			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
242			rb = mol->nextRigidBody(rbIter)) {
243	gezelter	1892	rb->updateAtomVel();
244	gezelter	1865	}
245			}
246	gezelter	1887
247			if (evaluator_.isDynamic()) {
248			seleMan_.setSelectionSet(evaluator_.evaluate());
249			}
250	gezelter	1865
251	gezelter	1887	// loop over the selected atoms:
252
253			for (sd = seleMan_.beginSelected(i); sd != NULL;
254			sd = seleMan_.nextSelected(i)) {
255	gezelter	1944
256	gezelter	1887	// figure out where that object is:
257	gezelter	1945	int bin = getBin( sd->getPos() );
258	gezelter	1865
259	gezelter	1944	if (bin >= 0 && bin < nBins_) {
260	gezelter	1887
261	gezelter	1944	Vector3d rPos = sd->getPos() - coordinateOrigin_;
262			Vector3d vel = sd->getVel();
263			RealType m = sd->getMass();
264			Vector3d L = m * cross(rPos, vel);
265			Mat3x3d I(0.0);
266			I = outProduct(rPos, rPos) * m;
267			RealType r2 = rPos.lengthSquare();
268			I(0, 0) += m * r2;
269			I(1, 1) += m * r2;
270			I(2, 2) += m * r2;
271	gezelter	1887
272	gezelter	1944	binMass[bin] += m;
273			binI[bin] += I;
274			binL[bin] += L;
275			binKE[bin] += 0.5 * (m * vel.lengthSquare());
276			binDof[bin] += 3;
277
278			if (sd->isDirectional()) {
279			Vector3d angMom = sd->getJ();
280			Mat3x3d Ia = sd->getI();
281			if (sd->isLinear()) {
282			int i = sd->linearAxis();
283			int j = (i + 1) % 3;
284			int k = (i + 2) % 3;
285			binKE[bin] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
286			angMom[k] * angMom[k] / Ia(k, k));
287			binDof[bin] += 2;
288			} else {
289			binKE[bin] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
290			angMom[1] * angMom[1] / Ia(1, 1) +
291			angMom[2] * angMom[2] / Ia(2, 2));
292			binDof[bin] += 3;
293			}
294	gezelter	1887	}
295			}
296			}
297	gezelter	1865
298	gezelter	1953	for (int i = 0; i < nBins_; i++) {
299	gezelter	1887	RealType rinner = (RealType)i * binWidth_;
300			RealType router = (RealType)(i+1) * binWidth_;
301			if (binDof[i] > 0) {
302			RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
303			PhysicalConstants::energyConvert);
304			RealType den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
305	gezelter	1944	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
306
307			Vector3d omega = binI[i].inverse() * binL[i];
308
309	gezelter	1887	dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
310	gezelter	1944	dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(omega);
311	gezelter	1887	dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
312			dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
313			}
314			}
315			}
316	gezelter	1865
317	gezelter	1887
318			void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
319	gezelter	1865	}
320	gezelter	1953
321			RNEMDRTheta::RNEMDRTheta(SimInfo* info, const std::string& filename,
322			const std::string& sele, int nrbins, int nangleBins)
323			: ShellStatistics(info, filename, sele, nrbins), nAngleBins_(nangleBins) {
324
325			Globals* simParams = info->getSimParams();
326			RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
327			bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
328
329			if (hasAngularMomentumFluxVector) {
330			fluxVector_ = rnemdParams->getAngularMomentumFluxVector();
331			} else {
332
333			std::string fluxStr = rnemdParams->getFluxType();
334			if (fluxStr.find("Lx") != std::string::npos) {
335			fluxVector_ = V3X;
336			} else if (fluxStr.find("Ly") != std::string::npos) {
337			fluxVector_ = V3Y;
338			} else {
339			fluxVector_ = V3Z;
340			}
341			}
342
343			fluxVector_.normalize();
344
345			setOutputName(getPrefix(filename) + ".rnemdRTheta");
346
347			angularVelocity = new OutputData;
348			angularVelocity->units = "angstroms^2/fs";
349			angularVelocity->title = "Angular Velocity";
350			angularVelocity->dataType = odtArray2d;
351			angularVelocity->dataHandling = odhAverage;
352			angularVelocity->accumulatorArray2d.reserve(nBins_);
353			for (int i = 0; i < nBins_; i++) {
354			angularVelocity->accumulatorArray2d[i].reserve(nAngleBins_);
355			for (int j = 0 ; j < nAngleBins_; j++) {
356			angularVelocity->accumulatorArray2d[i][j] = new Accumulator();
357			}
358			}
359			data_.push_back(angularVelocity);
360
361			}
362
363
364			std::pair<int,int> RNEMDRTheta::getBins(Vector3d pos) {
365			std::pair<int,int> result;
366
367			Vector3d rPos = pos - coordinateOrigin_;
368			RealType cosAngle= dot(rPos, fluxVector_) / rPos.length();
369
370			result.first = int(rPos.length() / binWidth_);
371			result.second = int( (nAngleBins_ - 1) * 0.5 * (cosAngle + 1.0) );
372			return result;
373			}
374
375			void RNEMDRTheta::processStuntDouble(StuntDouble* sd, int bin) {
376			}
377
378			void RNEMDRTheta::processFrame(int istep) {
379
380			Molecule* mol;
381			RigidBody* rb;
382			StuntDouble* sd;
383			SimInfo::MoleculeIterator mi;
384			Molecule::RigidBodyIterator rbIter;
385			int i;
386
387			vector<vector<Mat3x3d> > binI;
388			vector<vector<Vector3d> > binL;
389			vector<vector<int> > binCount;
390
391			for (mol = info_->beginMolecule(mi); mol != NULL;
392			mol = info_->nextMolecule(mi)) {
393
394			// change the positions of atoms which belong to the rigidbodies
395
396			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
397			rb = mol->nextRigidBody(rbIter)) {
398			rb->updateAtomVel();
399			}
400			}
401
402			if (evaluator_.isDynamic()) {
403			seleMan_.setSelectionSet(evaluator_.evaluate());
404			}
405
406			// loop over the selected atoms:
407
408			for (sd = seleMan_.beginSelected(i); sd != NULL;
409			sd = seleMan_.nextSelected(i)) {
410
411			// figure out where that object is:
412			std::pair<int,int> bins = getBins( sd->getPos() );
413
414			if (bins.first >= 0 && bins.first < nBins_) {
415			if (bins.second >= 0 && bins.second < nAngleBins_) {
416
417			Vector3d rPos = sd->getPos() - coordinateOrigin_;
418			Vector3d vel = sd->getVel();
419			RealType m = sd->getMass();
420			Vector3d L = m * cross(rPos, vel);
421			Mat3x3d I(0.0);
422			I = outProduct(rPos, rPos) * m;
423			RealType r2 = rPos.lengthSquare();
424			I(0, 0) += m * r2;
425			I(1, 1) += m * r2;
426			I(2, 2) += m * r2;
427
428			binI[bins.first][bins.second] += I;
429			binL[bins.first][bins.second] += L;
430			binCount[bins.first][bins.second]++;
431			}
432			}
433			}
434
435
436			for (int i = 0; i < nBins_; i++) {
437			for (int j = 0; j < nAngleBins_; j++) {
438
439			if (binCount[i][j] > 0) {
440			Vector3d omega = binI[i][j].inverse() * binL[i][j];
441			RealType omegaProj = dot(omega, fluxVector_);
442
443			dynamic_cast<Accumulator *>(angularVelocity->accumulatorArray2d[i][j])->add(omegaProj);
444			}
445			}
446			}
447			}
448
449			void RNEMDRTheta::writeOutput() {
450
451			vector<OutputData*>::iterator i;
452			OutputData* outputData;
453
454			ofstream outStream(outputFilename_.c_str());
455			if (outStream.is_open()) {
456
457			//write title
458			outStream << "# SPATIAL STATISTICS\n";
459			outStream << "#";
460
461			for(outputData = beginOutputData(i); outputData;
462			outputData = nextOutputData(i)) {
463			outStream << "\t" << outputData->title <<
464			"(" << outputData->units << ")";
465			// add some extra tabs for column alignment
466			if (outputData->dataType == odtVector3) outStream << "\t\t";
467			}
468
469			outStream << std::endl;
470
471			outStream.precision(8);
472
473			for (int j = 0; j < nBins_; j++) {
474
475			int counts = counts_->accumulator[j]->count();
476
477			if (counts > 0) {
478			for(outputData = beginOutputData(i); outputData;
479			outputData = nextOutputData(i)) {
480
481			int n = outputData->accumulator[j]->count();
482			if (n != 0) {
483			writeData( outStream, outputData, j );
484			}
485			}
486			outStream << std::endl;
487			}
488			}
489			}
490			}
491	gezelter	1865	}
492