applications/staticProps/Hxy.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 *
 *
 *  Hxy.cpp
 *  OOPSE-2.0
 *
 *  Created by Xiuquan Sun on 05/09/06.
 *  @author  Xiuquan Sun 
 *  @version $Id: Hxy.cpp,v 1.3 2006-05-16 20:38:23 gezelter Exp $
 *
 */

/* Calculates the undulation spectrum of the lipid membrance. */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/Hxy.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include<stdio.h>
#include<string.h>
#include<stdlib.h>
#include<math.h>

namespace oopse {
  
  Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins)
    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){

    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }

    gridsample_.resize(nBinsX_*nBinsY_);
    gridZ_.resize(nBinsX_*nBinsY_);

    sum_bin.resize(nbins_);
    avg_bin.resize(nbins_);
    errbin_sum.resize(nbins_);
    errbin.resize(nbins_);
    sum_bin_sq.resize(nbins_);
    avg_bin_sq.resize(nbins_);
    errbin_sum_sq.resize(nbins_);
    errbin_sq.resize(nbins_);

    setOutputName(getPrefix(filename) + ".Hxy");
  }

  void Hxy::process() {
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames/step_;
    
    std::vector<double> mag, newmag;
    double lenX_, lenY_;
    double gridX_, gridY_;
    double halfBoxX_, halfBoxY_;
    int binNoX, binNoY;
    double interpsum, value;
    int ninterp, px, py, newp;
    int newx, newy, newindex, index;
    int new_i, new_j, new_index;
    double freq_x, freq_y, zero_freq_x, zero_freq_y, freq;
    double maxfreqx, maxfreqy, maxfreq, dfreq;
    int whichbin;
    int nMolecules;
    
    for (int istep = 0; istep < nFrames; istep += step_) {
      
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      nMolecules = info_->getNGlobalMolecules();
      
      Mat3x3d hmat = currentSnapshot_->getHmat();
      
#ifdef HAVE_FFTW3_H
      fftw_plan p;
#else
      fftwnd_plan p;
#endif
      fftw_complex *in, *out;

      
      in = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * (nBinsX_*nBinsY_));
      out = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) *(nBinsX_*nBinsY_));

#ifdef HAVE_FFTW3_H
      p = fftw_plan_dft_2d(nBinsX_, nBinsY_, in, out, 
                           FFTW_FORWARD, FFTW_ESTIMATE); 
#else
      p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE);
#endif
      
      int i, j;   
      
      gridsample_.clear();
      gridZ_.clear();
      sum_bin.clear();
      avg_bin.clear();
      errbin_sum.clear();
      errbin.clear();
      sum_bin_sq.clear();
      avg_bin_sq.clear();
      errbin_sum_sq.clear();
      errbin_sq.clear();
      
      mag.resize(nBinsX_*nBinsY_);
      newmag.resize(nBinsX_*nBinsY_);     
      mag.clear();
      newmag.clear();
      
      StuntDouble* sd;
      
      lenX_ = hmat(0,0);
      lenY_ = hmat(1,1);
      
      gridX_ = lenX_ /(nBinsX_);
      gridY_ = lenY_ /(nBinsY_);
      
      double halfBoxX_ = lenX_ / 2.0;      
      double halfBoxY_ = lenY_ / 2.0;      
      
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
      
      //wrap the stuntdoubles into a cell     
      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        Vector3d pos = sd->getPos();
        currentSnapshot_->wrapVector(pos);
        sd->setPos(pos);
      }
      
      //determine which atom belongs to which grid
      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        Vector3d pos = sd->getPos();
        //int binNo = (pos.z() /deltaR_) - 1;
        int binNoX = (pos.x() + halfBoxX_) /gridX_; 
        int binNoY = (pos.y() + halfBoxY_) /gridY_;
        //std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = "  << deltaR_ << " binNo = " << binNo << "\n";
        gridZ_[binNoX*nBinsY_+binNoY] += pos.z();
        gridsample_[binNoX*nBinsY_+binNoY]++;
      }
      
      // FFT stuff depends on nx and ny, so delay allocation until we have
      // that information
      
      for (i=0; i< nBinsX_; i++) {
        for(j=0; j< nBinsY_; j++) {
          newindex = i*nBinsY_ + j;
          mag[newindex] = 0.0;
          newmag[newindex] = 0.0;
        }
      }
      
      for(i = 0; i < nBinsX_; i++){
        for(j = 0; j < nBinsY_; j++){
          newindex = i * nBinsY_ + j;
          if(gridsample_[newindex] > 0){
            gridZ_[newindex] = gridZ_[newindex] / (double)gridsample_[newindex];
          }
        }
      }
      
      for (i=0; i< nBinsX_; i++) {
        for(j=0; j< nBinsY_; j++) {
          newindex = i*nBinsY_ + j;
          if (gridsample_[newindex] == 0) {
            // interpolate from surrounding points:
            
            interpsum = 0.0;
            ninterp = 0;
            
            //point1 = bottom;
            
            px = i;
            py = j - 1;
            newp = px*nBinsY_ + py;
            if ((py >= 0) && (gridsample_[newp] > 0)) {
              interpsum += gridZ_[newp];
              ninterp++;
            } 
            
            //point2 = top;
            
            px = i;
            py = j + 1;
            newp = px*nBinsY_ + py;
            if ((py < nBinsY_) && (gridsample_[newp] > 0)) {
              interpsum += gridZ_[newp];
              ninterp++;
            } 
            
            //point3 = left;
            
            px = i - 1;
            py = j;
            newp = px*nBinsY_ + py;
            if ((px >= 0) && (gridsample_[newp] > 0)) {
              interpsum += gridZ_[newp];
              ninterp++;
            }
            
            //point4 = right;
            
            px = i + 1;
            py = j;
            newp = px*nBinsY_ + py;
            if ( (px < nBinsX_ ) && ( gridsample_[newp] > 0 )) { 
              interpsum += gridZ_[newp];
              ninterp++;
            } 
        
            value = interpsum / (double)ninterp;
            
            gridZ_[newindex] = value;
          }
        }
      }
      
      for (i=0; i < nBinsX_; i++) {
        for (j=0; j < nBinsY_; j++) {
          newindex = i*nBinsY_ + j;
          
          c_re(in[newindex]) = gridZ_[newindex];
          c_im(in[newindex]) = 0.0;
        } 
      }
#ifdef HAVE_FFTW3_H
      fftw_execute(p);
#else
      fftwnd_one(p, in, out);
#endif
      
      for (i=0; i< nBinsX_; i++) {
        for(j=0; j< nBinsY_; j++) {
          newindex = i*nBinsY_ + j;
          mag[newindex] = pow(c_re(out[newindex]),2) + pow(c_im(out[newindex]),2);
        }
      }
#ifdef HAVE_FFTW3_H
      fftw_destroy_plan(p);
#else
      fftwnd_destroy_plan(p);
#endif      
      fftw_free(out);
      fftw_free(in);

      for (i=0; i< (nBinsX_/2); i++) {
        for(j=0; j< (nBinsY_/2); j++) {
          index = i*nBinsY_ + j;
          new_i = i + (nBinsX_/2);
          new_j = j + (nBinsY_/2);
          new_index = new_i*nBinsY_ + new_j;
          newmag[new_index] = mag[index];
        }
      }
      
      for (i=(nBinsX_/2); i< nBinsX_; i++) {
        for(j=0; j< (nBinsY_/2); j++) {
          index = i*nBinsY_ + j;
          new_i = i - (nBinsX_/2);
          new_j = j + (nBinsY_/2);
          new_index = new_i*nBinsY_ + new_j;
          newmag[new_index] = mag[index];
        }
      }
      
      for (i=0; i< (nBinsX_/2); i++) {
        for(j=(nBinsY_/2); j< nBinsY_; j++) {
          index = i*nBinsY_ + j;
          new_i = i + (nBinsX_/2);
          new_j = j - (nBinsY_/2);
          new_index = new_i*nBinsY_ + new_j;
          newmag[new_index] = mag[index];
        }
      }
      
      for (i=(nBinsX_/2); i< nBinsX_; i++) {
        for(j=(nBinsY_/2); j< nBinsY_; j++) {
          index = i*nBinsY_ + j;
          new_i = i - (nBinsX_/2);
          new_j = j - (nBinsY_/2);
          new_index = new_i*nBinsY_ + new_j;
          newmag[new_index] = mag[index];
        }
      }
    
      maxfreqx = 1.0 / gridX_;
      maxfreqy = 1.0 / gridY_;
      
      //  printf("%lf\t%lf\t%lf\t%lf\n", dx, dy, maxfreqx, maxfreqy);
      
      maxfreq = sqrt(maxfreqx*maxfreqx + maxfreqy*maxfreqy);
      dfreq = maxfreq/(double)(nbins_-1);
    
      //printf("%lf\n", dfreq);
      
      zero_freq_x = nBinsX_/2; 
      zero_freq_y = nBinsY_/2; 
      
      for (i=0; i< nBinsX_; i++) {
        for(j=0; j< nBinsY_; j++) {
          
          freq_x = (double)(i - zero_freq_x)*maxfreqx*2 / nBinsX_;
          freq_y = (double)(j - zero_freq_y)*maxfreqy*2 / nBinsY_;
          
          freq = sqrt(freq_x*freq_x + freq_y*freq_y);
          
          whichbin = (int) (freq / dfreq);
          newindex = i*nBinsY_ + j;
          //    printf("%d %d %lf %lf\n", whichbin, newindex, freq, dfreq);
          bin[whichbin][istep] += newmag[newindex];
          samples[whichbin][istep]++;
        }
      }
      
      for ( i = 0; i < nbins_; i++) {
        if ( samples[i][istep] > 0) {
          bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (double)samples[i][istep]) / (double)nMolecules;
        }
      }    
      
    }
  
    for (int i = 0; i < nbins_; i++) {
      for (int j = 0; j < nFrames; j++) {
        sum_bin[i] += bin[i][j];
        sum_bin_sq[i] += bin[i][j] * bin[i][j];
      }
      avg_bin[i] = sum_bin[i] / (double)nFrames;
      avg_bin_sq[i] = sum_bin_sq[i] / (double)nFrames;
      for (int j = 0; j < nFrames; j++) {
        errbin_sum[i] += pow((bin[i][j] - avg_bin[i]), 2);
        errbin_sum_sq[i] += pow((bin[i][j] * bin[i][j] - avg_bin_sq[i]), 2);
      }
      errbin[i] = sqrt( errbin_sum[i] / (double)nFrames );
      errbin_sq[i] = sqrt( errbin_sum_sq[i] / (double)nFrames );
    }
    
    printSpectrum();
#else
    sprintf(painCave.errMsg, "Hxy: FFTW support was not compiled in!\n");
    painCave.isFatal = 1;
    simError();  

#endif

}
    
  void Hxy::printSpectrum() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      
      for (int i = 0; i < nbins_; i++) {
        if ( avg_bin[i] > 0 ){
          rdfStream << i*dfreq << "\t"
                    <<pow(avg_bin[i], 2)<<"\t"
                    <<errbin_sq[i]<<"\t"
                    <<avg_bin[i]<<"\t"
                    <<errbin[i]<<"\n";
        }
      }
    } else {
      
      sprintf(painCave.errMsg, "Hxy: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }
    
    rdfStream.close();
  }
  
}
Revision:	957
Committed:	Tue May 16 20:38:23 2006 UTC (18 years, 11 months ago) by gezelter
File size:	11922 byte(s)
Log Message:	Autoconf fixes for FFTW. Multiple FFTW version support.
#	User	Rev	Content
1	xsun	955	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*
41			*
42			* Hxy.cpp
43			* OOPSE-2.0
44			*
45			* Created by Xiuquan Sun on 05/09/06.
46			* @author Xiuquan Sun
47	gezelter	957	* @version $Id: Hxy.cpp,v 1.3 2006-05-16 20:38:23 gezelter Exp $
48	xsun	955	*
49			*/
50
51			/* Calculates the undulation spectrum of the lipid membrance. */
52
53			#include <algorithm>
54			#include <fstream>
55			#include "applications/staticProps/Hxy.hpp"
56			#include "utils/simError.h"
57			#include "io/DumpReader.hpp"
58			#include "primitives/Molecule.hpp"
59			#include<stdio.h>
60			#include<string.h>
61			#include<stdlib.h>
62			#include<math.h>
63
64			namespace oopse {
65
66			Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins)
67			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){
68
69			evaluator_.loadScriptString(sele);
70			if (!evaluator_.isDynamic()) {
71			seleMan_.setSelectionSet(evaluator_.evaluate());
72			}
73
74			gridsample_.resize(nBinsX_*nBinsY_);
75			gridZ_.resize(nBinsX_*nBinsY_);
76
77	gezelter	956	sum_bin.resize(nbins_);
78			avg_bin.resize(nbins_);
79			errbin_sum.resize(nbins_);
80			errbin.resize(nbins_);
81			sum_bin_sq.resize(nbins_);
82			avg_bin_sq.resize(nbins_);
83			errbin_sum_sq.resize(nbins_);
84			errbin_sq.resize(nbins_);
85	xsun	955
86			setOutputName(getPrefix(filename) + ".Hxy");
87			}
88
89			void Hxy::process() {
90	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
91	xsun	955	DumpReader reader(info_, dumpFilename_);
92			int nFrames = reader.getNFrames();
93			nProcessed_ = nFrames/step_;
94	gezelter	956
95	xsun	955	std::vector<double> mag, newmag;
96			double lenX_, lenY_;
97			double gridX_, gridY_;
98			double halfBoxX_, halfBoxY_;
99			int binNoX, binNoY;
100			double interpsum, value;
101			int ninterp, px, py, newp;
102			int newx, newy, newindex, index;
103			int new_i, new_j, new_index;
104			double freq_x, freq_y, zero_freq_x, zero_freq_y, freq;
105			double maxfreqx, maxfreqy, maxfreq, dfreq;
106			int whichbin;
107	gezelter	956	int nMolecules;
108	xsun	955
109			for (int istep = 0; istep < nFrames; istep += step_) {
110
111	gezelter	956	reader.readFrame(istep);
112			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
113			nMolecules = info_->getNGlobalMolecules();
114	gezelter	957
115	gezelter	956	Mat3x3d hmat = currentSnapshot_->getHmat();
116
117	gezelter	957	#ifdef HAVE_FFTW3_H
118			fftw_plan p;
119			#else
120			fftwnd_plan p;
121			#endif
122	xsun	955	fftw_complex in, out;
123	gezelter	957
124	gezelter	956
125			in = (fftw_complex) fftw_malloc(sizeof(fftw_complex) (nBinsX_*nBinsY_));
126			out = (fftw_complex) fftw_malloc(sizeof(fftw_complex) (nBinsX_*nBinsY_));
127	gezelter	957
128			#ifdef HAVE_FFTW3_H
129			p = fftw_plan_dft_2d(nBinsX_, nBinsY_, in, out,
130			FFTW_FORWARD, FFTW_ESTIMATE);
131			#else
132			p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE);
133			#endif
134	xsun	955
135			int i, j;
136	gezelter	956
137			gridsample_.clear();
138			gridZ_.clear();
139			sum_bin.clear();
140			avg_bin.clear();
141			errbin_sum.clear();
142			errbin.clear();
143			sum_bin_sq.clear();
144			avg_bin_sq.clear();
145			errbin_sum_sq.clear();
146			errbin_sq.clear();
147
148	xsun	955	mag.resize(nBinsX_*nBinsY_);
149	gezelter	956	newmag.resize(nBinsX_*nBinsY_);
150			mag.clear();
151			newmag.clear();
152	xsun	955
153			StuntDouble* sd;
154	gezelter	956
155	xsun	955	lenX_ = hmat(0,0);
156			lenY_ = hmat(1,1);
157	gezelter	956
158	xsun	955	gridX_ = lenX_ /(nBinsX_);
159			gridY_ = lenY_ /(nBinsY_);
160	gezelter	956
161	xsun	955	double halfBoxX_ = lenX_ / 2.0;
162			double halfBoxY_ = lenY_ / 2.0;
163	gezelter	956
164	xsun	955	if (evaluator_.isDynamic()) {
165			seleMan_.setSelectionSet(evaluator_.evaluate());
166			}
167
168			//wrap the stuntdoubles into a cell
169			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
170			Vector3d pos = sd->getPos();
171			currentSnapshot_->wrapVector(pos);
172			sd->setPos(pos);
173			}
174
175			//determine which atom belongs to which grid
176			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
177			Vector3d pos = sd->getPos();
178			//int binNo = (pos.z() /deltaR_) - 1;
179			int binNoX = (pos.x() + halfBoxX_) /gridX_;
180			int binNoY = (pos.y() + halfBoxY_) /gridY_;
181			//std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = " << deltaR_ << " binNo = " << binNo << "\n";
182			gridZ_[binNoX*nBinsY_+binNoY] += pos.z();
183			gridsample_[binNoX*nBinsY_+binNoY]++;
184			}
185
186			// FFT stuff depends on nx and ny, so delay allocation until we have
187			// that information
188
189			for (i=0; i< nBinsX_; i++) {
190			for(j=0; j< nBinsY_; j++) {
191			newindex = i*nBinsY_ + j;
192			mag[newindex] = 0.0;
193			newmag[newindex] = 0.0;
194			}
195			}
196
197			for(i = 0; i < nBinsX_; i++){
198			for(j = 0; j < nBinsY_; j++){
199			newindex = i * nBinsY_ + j;
200			if(gridsample_[newindex] > 0){
201			gridZ_[newindex] = gridZ_[newindex] / (double)gridsample_[newindex];
202			}
203			}
204			}
205	gezelter	956
206	xsun	955	for (i=0; i< nBinsX_; i++) {
207			for(j=0; j< nBinsY_; j++) {
208			newindex = i*nBinsY_ + j;
209			if (gridsample_[newindex] == 0) {
210			// interpolate from surrounding points:
211
212			interpsum = 0.0;
213			ninterp = 0;
214
215			//point1 = bottom;
216
217			px = i;
218			py = j - 1;
219			newp = px*nBinsY_ + py;
220			if ((py >= 0) && (gridsample_[newp] > 0)) {
221			interpsum += gridZ_[newp];
222			ninterp++;
223			}
224
225			//point2 = top;
226
227			px = i;
228			py = j + 1;
229			newp = px*nBinsY_ + py;
230			if ((py < nBinsY_) && (gridsample_[newp] > 0)) {
231			interpsum += gridZ_[newp];
232			ninterp++;
233			}
234
235			//point3 = left;
236
237			px = i - 1;
238			py = j;
239			newp = px*nBinsY_ + py;
240			if ((px >= 0) && (gridsample_[newp] > 0)) {
241			interpsum += gridZ_[newp];
242			ninterp++;
243			}
244
245			//point4 = right;
246
247			px = i + 1;
248			py = j;
249			newp = px*nBinsY_ + py;
250	gezelter	956	if ( (px < nBinsX_ ) && ( gridsample_[newp] > 0 )) {
251			interpsum += gridZ_[newp];
252			ninterp++;
253			}
254
255	xsun	955	value = interpsum / (double)ninterp;
256
257			gridZ_[newindex] = value;
258			}
259			}
260			}
261
262			for (i=0; i < nBinsX_; i++) {
263			for (j=0; j < nBinsY_; j++) {
264			newindex = i*nBinsY_ + j;
265
266			c_re(in[newindex]) = gridZ_[newindex];
267			c_im(in[newindex]) = 0.0;
268			}
269			}
270	gezelter	957	#ifdef HAVE_FFTW3_H
271			fftw_execute(p);
272			#else
273			fftwnd_one(p, in, out);
274			#endif
275	xsun	955
276			for (i=0; i< nBinsX_; i++) {
277			for(j=0; j< nBinsY_; j++) {
278			newindex = i*nBinsY_ + j;
279			mag[newindex] = pow(c_re(out[newindex]),2) + pow(c_im(out[newindex]),2);
280			}
281			}
282	gezelter	957	#ifdef HAVE_FFTW3_H
283	xsun	955	fftw_destroy_plan(p);
284	gezelter	957	#else
285			fftwnd_destroy_plan(p);
286			#endif
287	xsun	955	fftw_free(out);
288			fftw_free(in);
289
290			for (i=0; i< (nBinsX_/2); i++) {
291			for(j=0; j< (nBinsY_/2); j++) {
292			index = i*nBinsY_ + j;
293			new_i = i + (nBinsX_/2);
294			new_j = j + (nBinsY_/2);
295			new_index = new_i*nBinsY_ + new_j;
296			newmag[new_index] = mag[index];
297			}
298			}
299
300			for (i=(nBinsX_/2); i< nBinsX_; i++) {
301			for(j=0; j< (nBinsY_/2); j++) {
302			index = i*nBinsY_ + j;
303			new_i = i - (nBinsX_/2);
304			new_j = j + (nBinsY_/2);
305			new_index = new_i*nBinsY_ + new_j;
306			newmag[new_index] = mag[index];
307			}
308			}
309
310			for (i=0; i< (nBinsX_/2); i++) {
311			for(j=(nBinsY_/2); j< nBinsY_; j++) {
312			index = i*nBinsY_ + j;
313			new_i = i + (nBinsX_/2);
314			new_j = j - (nBinsY_/2);
315			new_index = new_i*nBinsY_ + new_j;
316			newmag[new_index] = mag[index];
317			}
318			}
319
320			for (i=(nBinsX_/2); i< nBinsX_; i++) {
321			for(j=(nBinsY_/2); j< nBinsY_; j++) {
322			index = i*nBinsY_ + j;
323			new_i = i - (nBinsX_/2);
324			new_j = j - (nBinsY_/2);
325			new_index = new_i*nBinsY_ + new_j;
326			newmag[new_index] = mag[index];
327			}
328			}
329
330			maxfreqx = 1.0 / gridX_;
331			maxfreqy = 1.0 / gridY_;
332
333			// printf("%lf\t%lf\t%lf\t%lf\n", dx, dy, maxfreqx, maxfreqy);
334
335			maxfreq = sqrt(maxfreqxmaxfreqx + maxfreqymaxfreqy);
336	gezelter	956	dfreq = maxfreq/(double)(nbins_-1);
337	xsun	955
338			//printf("%lf\n", dfreq);
339
340			zero_freq_x = nBinsX_/2;
341			zero_freq_y = nBinsY_/2;
342
343			for (i=0; i< nBinsX_; i++) {
344			for(j=0; j< nBinsY_; j++) {
345
346			freq_x = (double)(i - zero_freq_x)maxfreqx2 / nBinsX_;
347			freq_y = (double)(j - zero_freq_y)maxfreqy2 / nBinsY_;
348
349			freq = sqrt(freq_xfreq_x + freq_yfreq_y);
350
351			whichbin = (int) (freq / dfreq);
352			newindex = i*nBinsY_ + j;
353			// printf("%d %d %lf %lf\n", whichbin, newindex, freq, dfreq);
354			bin[whichbin][istep] += newmag[newindex];
355			samples[whichbin][istep]++;
356			}
357			}
358
359	gezelter	956	for ( i = 0; i < nbins_; i++) {
360	xsun	955	if ( samples[i][istep] > 0) {
361			bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (double)samples[i][istep]) / (double)nMolecules;
362			}
363			}
364
365			}
366
367	gezelter	956	for (int i = 0; i < nbins_; i++) {
368			for (int j = 0; j < nFrames; j++) {
369	xsun	955	sum_bin[i] += bin[i][j];
370			sum_bin_sq[i] += bin[i][j] * bin[i][j];
371			}
372			avg_bin[i] = sum_bin[i] / (double)nFrames;
373			avg_bin_sq[i] = sum_bin_sq[i] / (double)nFrames;
374	gezelter	956	for (int j = 0; j < nFrames; j++) {
375	xsun	955	errbin_sum[i] += pow((bin[i][j] - avg_bin[i]), 2);
376			errbin_sum_sq[i] += pow((bin[i][j] * bin[i][j] - avg_bin_sq[i]), 2);
377			}
378			errbin[i] = sqrt( errbin_sum[i] / (double)nFrames );
379			errbin_sq[i] = sqrt( errbin_sum_sq[i] / (double)nFrames );
380			}
381	gezelter	956
382			printSpectrum();
383			#else
384			sprintf(painCave.errMsg, "Hxy: FFTW support was not compiled in!\n");
385			painCave.isFatal = 1;
386			simError();
387	xsun	955
388	gezelter	956	#endif
389
390			}
391	xsun	955
392			void Hxy::printSpectrum() {
393			std::ofstream rdfStream(outputFilename_.c_str());
394			if (rdfStream.is_open()) {
395
396	gezelter	956	for (int i = 0; i < nbins_; i++) {
397	xsun	955	if ( avg_bin[i] > 0 ){
398			rdfStream << i*dfreq << "\t"
399			<<pow(avg_bin[i], 2)<<"\t"
400			<<errbin_sq[i]<<"\t"
401			<<avg_bin[i]<<"\t"
402			<<errbin[i]<<"\n";
403			}
404			}
405			} else {
406
407			sprintf(painCave.errMsg, "Hxy: unable to open %s\n", outputFilename_.c_str());
408			painCave.isFatal = 1;
409			simError();
410			}
411
412			rdfStream.close();
413			}
414
415			}