applications/staticProps/TetrahedralityParamXYZ.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).
 * [6]  Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 */
 
#include "applications/staticProps/TetrahedralityParamXYZ.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include <vector>
#include <algorithm>
#include <fstream>

using namespace std;
namespace OpenMD {
  TetrahedralityParamXYZ::TetrahedralityParamXYZ(SimInfo* info,  
                                                 const std::string& filename, 
                                                 const std::string& sele1,
                                                 const std::string& sele2,
                                                 RealType rCut, 
                                                 RealType voxelSize,
                                                 RealType gaussWidth) 
    : StaticAnalyser(info, filename), selectionScript1_(sele1), 
      evaluator1_(info), seleMan1_(info), selectionScript2_(sele2), 
      evaluator2_(info), seleMan2_(info), rCut_(rCut), voxelSize_(voxelSize),
      gaussWidth_(gaussWidth) {
    
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    evaluator2_.loadScriptString(sele2);
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }
    
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();

    nBins_(0) = int(hmat(0,0) / voxelSize);
    nBins_(1) = int(hmat(1,1) / voxelSize);
    nBins_(2) = int(hmat(2,2) / voxelSize);

    hist_.resize(nBins_(0));
    count_.resize(nBins_(0));
    for (int i = 0 ; i < nBins_(0); ++i) {
      hist_[i].resize(nBins_(1));
      count_[i].resize(nBins_(1));
      for(int j = 0; j < nBins_(1); ++j) {
        hist_[i][j].resize(nBins_(2));
        count_[i][j].resize(nBins_(2));
        std::fill(hist_[i][j].begin(), hist_[i][j].end(), 0.0);
        std::fill(count_[i][j].begin(), count_[i][j].end(), 0.0);

      }
    }   
    
    setOutputName(getPrefix(filename) + ".Qxyz");
  }
  
  TetrahedralityParamXYZ::~TetrahedralityParamXYZ() {
  }
    
  void TetrahedralityParamXYZ::process() {
    Molecule* mol;
    StuntDouble* sd;
    StuntDouble* sd2;
    StuntDouble* sdi;
    StuntDouble* sdj;
    RigidBody* rb;
    int myIndex;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Vector3d vec;
    Vector3d ri, rj, rk, rik, rkj;
    RealType r;
    RealType cospsi;
    RealType Qk;
    std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
    //std::vector<std::pair<Vector3d, RealType> > qvals;
    //std::vector<std::pair<Vector3d, RealType> >::iterator qiter;
    int isd1;
    int isd2;


    int kMax = int(5.0 * gaussWidth_ / voxelSize_);
    int kSqLim = kMax*kMax;
    cerr << "gw = " << gaussWidth_ << " vS = " << voxelSize_ << " kMax = " << kMax << " kSqLim = " << kSqLim << "\n";
    
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);

      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      Mat3x3d hmat = currentSnapshot_->getHmat();
      Vector3d halfBox = Vector3d(hmat(0,0), hmat(1,1), hmat(2,2)) / 2.0;

      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
      
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
      }
      
      // update the positions of atoms which belong to the rigidbodies
      for (mol = info_->beginMolecule(mi); mol != NULL;
           mol = info_->nextMolecule(mi)) {
        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }
      }
      
      //qvals.clear();

      // outer loop is over the selected StuntDoubles:
      for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
           sd = seleMan1_.nextSelected(isd1)) {
        
        myIndex = sd->getGlobalIndex();
        
        Qk = 1.0;         
        myNeighbors.clear();       

        for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
             sd2 = seleMan2_.nextSelected(isd2)) {
          
          if (sd2->getGlobalIndex() != myIndex) {
            
            vec = sd->getPos() - sd2->getPos();       
            
            if (usePeriodicBoundaryConditions_) 
              currentSnapshot_->wrapVector(vec);
            
            r = vec.length();             
            
            // Check to see if neighbor is in bond cutoff 
            
            if (r < rCut_) {                
              myNeighbors.push_back(std::make_pair(r,sd2));
            }
          }
        }
        
        // Sort the vector using predicate and std::sort
        std::sort(myNeighbors.begin(), myNeighbors.end());
        
        // Use only the 4 closest neighbors to do the rest of the work:
        
        int nbors =  myNeighbors.size()> 4 ? 4 : myNeighbors.size();
        int nang = int (0.5 * (nbors * (nbors - 1)));
        
        rk = sd->getPos();
        
        for (int i = 0; i < nbors-1; i++) {       
          
          sdi = myNeighbors[i].second;
          ri = sdi->getPos();
          rik = rk - ri;
          if (usePeriodicBoundaryConditions_) 
            currentSnapshot_->wrapVector(rik);
          
          rik.normalize();
          
          for (int j = i+1; j < nbors; j++) {       
            
            sdj = myNeighbors[j].second;
            rj = sdj->getPos();
            rkj = rk - rj;
            if (usePeriodicBoundaryConditions_) 
              currentSnapshot_->wrapVector(rkj);
            rkj.normalize();
            
            cospsi = dot(rik,rkj);           
            
            // Calculates scaled Qk for each molecule using calculated
            // angles from 4 or fewer nearest neighbors.
            Qk -=  (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);            
          }
        }
        
        if (nang > 0) {
          if (usePeriodicBoundaryConditions_)
            currentSnapshot_->wrapVector(rk);
          //qvals.push_back(std::make_pair(rk, Qk));
          
          Vector3d pos = rk + halfBox;


          Vector3i whichVoxel(int(pos[0] / voxelSize_), 
                              int(pos[1] / voxelSize_), 
                              int(pos[2] / voxelSize_));
          
          for (int l = -kMax; l <= kMax; l++) {
            for (int m = -kMax; m <= kMax; m++) {
              for (int n = -kMax; n <= kMax; n++) {
                int kk = l*l + m*m + n*n;
                if(kk <= kSqLim) {

                  int ll = (whichVoxel[0] + l) % nBins_(0);
                  ll = ll < 0 ? nBins_(0) + ll : ll;
                  int mm = (whichVoxel[1] + m) % nBins_(1);
                  mm = mm < 0 ? nBins_(1) + mm : mm;
                  int nn = (whichVoxel[2] + n) % nBins_(2);
                  nn = nn < 0 ? nBins_(2) + nn : nn;

                  Vector3d bPos = Vector3d(ll,mm,nn) * voxelSize_ - halfBox;
                  Vector3d d = bPos - rk;
                  currentSnapshot_->wrapVector(d);
                  RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
                  RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
                  RealType weight = exp(exponent) / denom;
                  count_[ll][mm][nn] += weight;
                  hist_[ll][mm][nn] += weight * Qk;
                }
              }
            }
          }
        }
      }

      // for (int i = 0; i < nBins_(0); ++i) {
      //   for(int j = 0; j < nBins_(1); ++j) {
      //     for(int k = 0; k < nBins_(2); ++k) {
      //       Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox;
      //       for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) {
      //         Vector3d d = pos - (*qiter).first;
      //         currentSnapshot_->wrapVector(d);
      //         RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
      //         RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
      //         RealType weight = exp(exponent) / denom;
      //         count_[i][j][k] += weight;
      //         hist_[i][j][k] += weight * (*qiter).second;
      //       }
      //     }
      //   }
      // }
    }
    writeQxyz();
  }
  
  void TetrahedralityParamXYZ::writeQxyz() {

    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();

    // normalize by total weight in voxel:
    for (unsigned int i = 0; i < hist_.size(); ++i) { 
      for(unsigned int j = 0; j < hist_[i].size(); ++j) { 
        for(unsigned int k = 0;k < hist_[i][j].size(); ++k) {
          hist_[i][j][k] = hist_[i][j][k] / count_[i][j][k];
        }
      }
    }

    std::ofstream qXYZstream(outputFilename_.c_str());
    if (qXYZstream.is_open()) {
      qXYZstream <<  "# AmiraMesh ASCII 1.0\n\n";
      qXYZstream <<  "# Dimensions in x-, y-, and z-direction\n";
      qXYZstream <<  "  define Lattice " << hist_.size() << " " << hist_[0].size() << " " << hist_[0][0].size() << "\n";
      
      qXYZstream <<  "Parameters {\n";
      qXYZstream <<  "    CoordType \"uniform\",\n";
      qXYZstream <<  "    # BoundingBox is xmin xmax ymin ymax zmin zmax\n";
      qXYZstream <<  "    BoundingBox 0.0 " << hmat(0,0) << 
        " 0.0 " << hmat(1,1) << 
        " 0.0 " << hmat(2,2) << "\n";
      qXYZstream <<  "}\n";
      
      qXYZstream <<  "Lattice { double ScalarField } = @1\n";
      
      qXYZstream <<  "@1\n";

      int xsize = hist_.size();
      int ysize = hist_[0].size();
      int zsize = hist_[0][0].size();
      
      for (unsigned int k = 0; k < zsize; ++k) { 
        for(unsigned int j = 0; j < ysize; ++j) { 
          for(unsigned int i = 0; i < xsize; ++i) {
            qXYZstream << hist_[i][j][k] << " ";

            //qXYZstream.write(reinterpret_cast<char *>( &hist_[i][j][k] ),
            // sizeof( hist_[i][j][k] ));
          }
        }
      }
      
    } else {      
      sprintf(painCave.errMsg, "TetrahedralityParamXYZ: unable to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }    
    qXYZstream.close();
  }
}


Revision:	2017
Committed:	Tue Sep 2 18:31:44 2014 UTC (10 years, 8 months ago) by gezelter
File size:	12476 byte(s)
Log Message:	Latest
#	User	Rev	Content
1	gezelter	2015	/*
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			* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
42			*/
43
44			#include "applications/staticProps/TetrahedralityParamXYZ.hpp"
45			#include "utils/simError.h"
46			#include "io/DumpReader.hpp"
47			#include "primitives/Molecule.hpp"
48			#include "utils/NumericConstant.hpp"
49			#include <vector>
50			#include <algorithm>
51			#include <fstream>
52
53			using namespace std;
54			namespace OpenMD {
55			TetrahedralityParamXYZ::TetrahedralityParamXYZ(SimInfo* info,
56			const std::string& filename,
57			const std::string& sele1,
58			const std::string& sele2,
59	gezelter	2017	RealType rCut,
60			RealType voxelSize,
61	gezelter	2015	RealType gaussWidth)
62			: StaticAnalyser(info, filename), selectionScript1_(sele1),
63			evaluator1_(info), seleMan1_(info), selectionScript2_(sele2),
64			evaluator2_(info), seleMan2_(info), rCut_(rCut), voxelSize_(voxelSize),
65			gaussWidth_(gaussWidth) {
66
67			evaluator1_.loadScriptString(sele1);
68			if (!evaluator1_.isDynamic()) {
69			seleMan1_.setSelectionSet(evaluator1_.evaluate());
70			}
71			evaluator2_.loadScriptString(sele2);
72			if (!evaluator2_.isDynamic()) {
73			seleMan2_.setSelectionSet(evaluator2_.evaluate());
74			}
75
76			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
77
78			nBins_(0) = int(hmat(0,0) / voxelSize);
79			nBins_(1) = int(hmat(1,1) / voxelSize);
80			nBins_(2) = int(hmat(2,2) / voxelSize);
81
82			hist_.resize(nBins_(0));
83			count_.resize(nBins_(0));
84			for (int i = 0 ; i < nBins_(0); ++i) {
85			hist_[i].resize(nBins_(1));
86			count_[i].resize(nBins_(1));
87			for(int j = 0; j < nBins_(1); ++j) {
88			hist_[i][j].resize(nBins_(2));
89			count_[i][j].resize(nBins_(2));
90			std::fill(hist_[i][j].begin(), hist_[i][j].end(), 0.0);
91			std::fill(count_[i][j].begin(), count_[i][j].end(), 0.0);
92
93			}
94			}
95
96			setOutputName(getPrefix(filename) + ".Qxyz");
97			}
98
99			TetrahedralityParamXYZ::~TetrahedralityParamXYZ() {
100			}
101
102			void TetrahedralityParamXYZ::process() {
103			Molecule* mol;
104			StuntDouble* sd;
105			StuntDouble* sd2;
106			StuntDouble* sdi;
107			StuntDouble* sdj;
108			RigidBody* rb;
109			int myIndex;
110			SimInfo::MoleculeIterator mi;
111			Molecule::RigidBodyIterator rbIter;
112			Vector3d vec;
113			Vector3d ri, rj, rk, rik, rkj;
114			RealType r;
115			RealType cospsi;
116			RealType Qk;
117			std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
118	gezelter	2017	//std::vector<std::pair<Vector3d, RealType> > qvals;
119			//std::vector<std::pair<Vector3d, RealType> >::iterator qiter;
120	gezelter	2015	int isd1;
121			int isd2;
122
123	gezelter	2017
124			int kMax = int(5.0 * gaussWidth_ / voxelSize_);
125			int kSqLim = kMax*kMax;
126			cerr << "gw = " << gaussWidth_ << " vS = " << voxelSize_ << " kMax = " << kMax << " kSqLim = " << kSqLim << "\n";
127
128	gezelter	2015	DumpReader reader(info_, dumpFilename_);
129			int nFrames = reader.getNFrames();
130
131			for (int istep = 0; istep < nFrames; istep += step_) {
132			reader.readFrame(istep);
133
134	plouden	2016	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
135			Mat3x3d hmat = currentSnapshot_->getHmat();
136			Vector3d halfBox = Vector3d(hmat(0,0), hmat(1,1), hmat(2,2)) / 2.0;
137
138	gezelter	2015	if (evaluator1_.isDynamic()) {
139			seleMan1_.setSelectionSet(evaluator1_.evaluate());
140			}
141
142			if (evaluator2_.isDynamic()) {
143			seleMan2_.setSelectionSet(evaluator2_.evaluate());
144			}
145
146			// update the positions of atoms which belong to the rigidbodies
147			for (mol = info_->beginMolecule(mi); mol != NULL;
148			mol = info_->nextMolecule(mi)) {
149			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
150			rb = mol->nextRigidBody(rbIter)) {
151			rb->updateAtoms();
152			}
153			}
154
155	gezelter	2017	//qvals.clear();
156	gezelter	2015
157			// outer loop is over the selected StuntDoubles:
158			for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
159			sd = seleMan1_.nextSelected(isd1)) {
160
161			myIndex = sd->getGlobalIndex();
162
163			Qk = 1.0;
164			myNeighbors.clear();
165
166			for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
167			sd2 = seleMan2_.nextSelected(isd2)) {
168
169			if (sd2->getGlobalIndex() != myIndex) {
170
171			vec = sd->getPos() - sd2->getPos();
172
173			if (usePeriodicBoundaryConditions_)
174			currentSnapshot_->wrapVector(vec);
175
176			r = vec.length();
177
178			// Check to see if neighbor is in bond cutoff
179
180			if (r < rCut_) {
181			myNeighbors.push_back(std::make_pair(r,sd2));
182			}
183			}
184			}
185
186			// Sort the vector using predicate and std::sort
187			std::sort(myNeighbors.begin(), myNeighbors.end());
188
189			// Use only the 4 closest neighbors to do the rest of the work:
190
191			int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size();
192			int nang = int (0.5 * (nbors * (nbors - 1)));
193
194			rk = sd->getPos();
195
196			for (int i = 0; i < nbors-1; i++) {
197
198			sdi = myNeighbors[i].second;
199			ri = sdi->getPos();
200			rik = rk - ri;
201			if (usePeriodicBoundaryConditions_)
202			currentSnapshot_->wrapVector(rik);
203
204			rik.normalize();
205
206			for (int j = i+1; j < nbors; j++) {
207
208			sdj = myNeighbors[j].second;
209			rj = sdj->getPos();
210			rkj = rk - rj;
211			if (usePeriodicBoundaryConditions_)
212			currentSnapshot_->wrapVector(rkj);
213			rkj.normalize();
214
215			cospsi = dot(rik,rkj);
216
217			// Calculates scaled Qk for each molecule using calculated
218			// angles from 4 or fewer nearest neighbors.
219			Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
220			}
221			}
222
223			if (nang > 0) {
224			if (usePeriodicBoundaryConditions_)
225			currentSnapshot_->wrapVector(rk);
226	gezelter	2017	//qvals.push_back(std::make_pair(rk, Qk));
227
228			Vector3d pos = rk + halfBox;
229	gezelter	2015
230	gezelter	2017
231			Vector3i whichVoxel(int(pos[0] / voxelSize_),
232			int(pos[1] / voxelSize_),
233			int(pos[2] / voxelSize_));
234
235			for (int l = -kMax; l <= kMax; l++) {
236			for (int m = -kMax; m <= kMax; m++) {
237			for (int n = -kMax; n <= kMax; n++) {
238			int kk = ll + mm + n*n;
239			if(kk <= kSqLim) {
240
241			int ll = (whichVoxel[0] + l) % nBins_(0);
242			ll = ll < 0 ? nBins_(0) + ll : ll;
243			int mm = (whichVoxel[1] + m) % nBins_(1);
244			mm = mm < 0 ? nBins_(1) + mm : mm;
245			int nn = (whichVoxel[2] + n) % nBins_(2);
246			nn = nn < 0 ? nBins_(2) + nn : nn;
247
248			Vector3d bPos = Vector3d(ll,mm,nn) * voxelSize_ - halfBox;
249			Vector3d d = bPos - rk;
250			currentSnapshot_->wrapVector(d);
251			RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
252			RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
253			RealType weight = exp(exponent) / denom;
254			count_[ll][mm][nn] += weight;
255			hist_[ll][mm][nn] += weight * Qk;
256			}
257			}
258	gezelter	2015	}
259			}
260			}
261			}
262	gezelter	2017
263			// for (int i = 0; i < nBins_(0); ++i) {
264			// for(int j = 0; j < nBins_(1); ++j) {
265			// for(int k = 0; k < nBins_(2); ++k) {
266			// Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox;
267			// for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) {
268			// Vector3d d = pos - (*qiter).first;
269			// currentSnapshot_->wrapVector(d);
270			// RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
271			// RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
272			// RealType weight = exp(exponent) / denom;
273			// count_[i][j][k] += weight;
274			// hist_[i][j][k] += weight * (*qiter).second;
275			// }
276			// }
277			// }
278			// }
279	gezelter	2015	}
280			writeQxyz();
281			}
282
283			void TetrahedralityParamXYZ::writeQxyz() {
284	plouden	2016
285			Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
286
287	gezelter	2015	// normalize by total weight in voxel:
288			for (unsigned int i = 0; i < hist_.size(); ++i) {
289			for(unsigned int j = 0; j < hist_[i].size(); ++j) {
290			for(unsigned int k = 0;k < hist_[i][j].size(); ++k) {
291	plouden	2016	hist_[i][j][k] = hist_[i][j][k] / count_[i][j][k];
292	gezelter	2015	}
293			}
294			}
295
296			std::ofstream qXYZstream(outputFilename_.c_str());
297			if (qXYZstream.is_open()) {
298	plouden	2016	qXYZstream << "# AmiraMesh ASCII 1.0\n\n";
299			qXYZstream << "# Dimensions in x-, y-, and z-direction\n";
300			qXYZstream << " define Lattice " << hist_.size() << " " << hist_[0].size() << " " << hist_[0][0].size() << "\n";
301
302			qXYZstream << "Parameters {\n";
303			qXYZstream << " CoordType \"uniform\",\n";
304			qXYZstream << " # BoundingBox is xmin xmax ymin ymax zmin zmax\n";
305			qXYZstream << " BoundingBox 0.0 " << hmat(0,0) <<
306			" 0.0 " << hmat(1,1) <<
307			" 0.0 " << hmat(2,2) << "\n";
308			qXYZstream << "}\n";
309
310			qXYZstream << "Lattice { double ScalarField } = @1\n";
311
312			qXYZstream << "@1\n";
313	gezelter	2015
314	plouden	2016	int xsize = hist_.size();
315			int ysize = hist_[0].size();
316			int zsize = hist_[0][0].size();
317
318			for (unsigned int k = 0; k < zsize; ++k) {
319			for(unsigned int j = 0; j < ysize; ++j) {
320			for(unsigned int i = 0; i < xsize; ++i) {
321			qXYZstream << hist_[i][j][k] << " ";
322
323			//qXYZstream.write(reinterpret_cast<char *>( &hist_[i][j][k] ),
324			// sizeof( hist_[i][j][k] ));
325	gezelter	2015	}
326			}
327			}
328
329			} else {
330			sprintf(painCave.errMsg, "TetrahedralityParamXYZ: unable to open %s\n",
331			outputFilename_.c_str());
332			painCave.isFatal = 1;
333			simError();
334			}
335			qXYZstream.close();
336			}
337			}
338
339
340