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 1.2 2006-05-16 02:06:37 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>
#ifndef WITHOUT_FFTW
#include<fftw3.h>
#endif

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() {
#ifndef WITHOUT_FFTW  

    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();

      
      fftw_complex *in, *out;
      fftw_plan p;
      
      in = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * (nBinsX_*nBinsY_));
      out = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) *(nBinsX_*nBinsY_));
      p =  fftw_plan_dft_2d(nBinsX_, 
                            nBinsY_, 
                            in, out,
                            FFTW_FORWARD, 
                            FFTW_ESTIMATE);
      
      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;
        } 
      }
      
      fftw_execute(p); 
      
      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);
        }
      }
      
      fftw_destroy_plan(p);
      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:	956
Committed:	Tue May 16 02:06:37 2006 UTC (18 years, 11 months ago) by gezelter
File size:	11632 byte(s)
Log Message:	* empty log message *
#	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	956	* @version $Id: Hxy.cpp,v 1.2 2006-05-16 02:06:37 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	gezelter	956	#ifndef WITHOUT_FFTW
64	xsun	955	#include<fftw3.h>
65	gezelter	956	#endif
66	xsun	955
67			namespace oopse {
68
69			Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins)
70			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){
71
72			evaluator_.loadScriptString(sele);
73			if (!evaluator_.isDynamic()) {
74			seleMan_.setSelectionSet(evaluator_.evaluate());
75			}
76
77			gridsample_.resize(nBinsX_*nBinsY_);
78			gridZ_.resize(nBinsX_*nBinsY_);
79
80	gezelter	956	sum_bin.resize(nbins_);
81			avg_bin.resize(nbins_);
82			errbin_sum.resize(nbins_);
83			errbin.resize(nbins_);
84			sum_bin_sq.resize(nbins_);
85			avg_bin_sq.resize(nbins_);
86			errbin_sum_sq.resize(nbins_);
87			errbin_sq.resize(nbins_);
88	xsun	955
89			setOutputName(getPrefix(filename) + ".Hxy");
90			}
91
92			void Hxy::process() {
93	gezelter	956	#ifndef WITHOUT_FFTW
94
95	xsun	955	DumpReader reader(info_, dumpFilename_);
96			int nFrames = reader.getNFrames();
97			nProcessed_ = nFrames/step_;
98	gezelter	956
99	xsun	955	std::vector<double> mag, newmag;
100			double lenX_, lenY_;
101			double gridX_, gridY_;
102			double halfBoxX_, halfBoxY_;
103			int binNoX, binNoY;
104			double interpsum, value;
105			int ninterp, px, py, newp;
106			int newx, newy, newindex, index;
107			int new_i, new_j, new_index;
108			double freq_x, freq_y, zero_freq_x, zero_freq_y, freq;
109			double maxfreqx, maxfreqy, maxfreq, dfreq;
110			int whichbin;
111	gezelter	956	int nMolecules;
112	xsun	955
113			for (int istep = 0; istep < nFrames; istep += step_) {
114
115	gezelter	956	reader.readFrame(istep);
116			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
117			nMolecules = info_->getNGlobalMolecules();
118	xsun	955
119	gezelter	956	Mat3x3d hmat = currentSnapshot_->getHmat();
120
121
122	xsun	955	fftw_complex in, out;
123			fftw_plan p;
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	xsun	955	p = fftw_plan_dft_2d(nBinsX_,
128			nBinsY_,
129			in, out,
130			FFTW_FORWARD,
131			FFTW_ESTIMATE);
132
133			int i, j;
134	gezelter	956
135			gridsample_.clear();
136			gridZ_.clear();
137			sum_bin.clear();
138			avg_bin.clear();
139			errbin_sum.clear();
140			errbin.clear();
141			sum_bin_sq.clear();
142			avg_bin_sq.clear();
143			errbin_sum_sq.clear();
144			errbin_sq.clear();
145
146	xsun	955	mag.resize(nBinsX_*nBinsY_);
147	gezelter	956	newmag.resize(nBinsX_*nBinsY_);
148			mag.clear();
149			newmag.clear();
150	xsun	955
151			StuntDouble* sd;
152	gezelter	956
153	xsun	955	lenX_ = hmat(0,0);
154			lenY_ = hmat(1,1);
155	gezelter	956
156	xsun	955	gridX_ = lenX_ /(nBinsX_);
157			gridY_ = lenY_ /(nBinsY_);
158	gezelter	956
159	xsun	955	double halfBoxX_ = lenX_ / 2.0;
160			double halfBoxY_ = lenY_ / 2.0;
161	gezelter	956
162	xsun	955	if (evaluator_.isDynamic()) {
163			seleMan_.setSelectionSet(evaluator_.evaluate());
164			}
165
166			//wrap the stuntdoubles into a cell
167			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
168			Vector3d pos = sd->getPos();
169			currentSnapshot_->wrapVector(pos);
170			sd->setPos(pos);
171			}
172
173			//determine which atom belongs to which grid
174			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
175			Vector3d pos = sd->getPos();
176			//int binNo = (pos.z() /deltaR_) - 1;
177			int binNoX = (pos.x() + halfBoxX_) /gridX_;
178			int binNoY = (pos.y() + halfBoxY_) /gridY_;
179			//std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = " << deltaR_ << " binNo = " << binNo << "\n";
180			gridZ_[binNoX*nBinsY_+binNoY] += pos.z();
181			gridsample_[binNoX*nBinsY_+binNoY]++;
182			}
183
184			// FFT stuff depends on nx and ny, so delay allocation until we have
185			// that information
186
187			for (i=0; i< nBinsX_; i++) {
188			for(j=0; j< nBinsY_; j++) {
189			newindex = i*nBinsY_ + j;
190			mag[newindex] = 0.0;
191			newmag[newindex] = 0.0;
192			}
193			}
194
195			for(i = 0; i < nBinsX_; i++){
196			for(j = 0; j < nBinsY_; j++){
197			newindex = i * nBinsY_ + j;
198			if(gridsample_[newindex] > 0){
199			gridZ_[newindex] = gridZ_[newindex] / (double)gridsample_[newindex];
200			}
201			}
202			}
203	gezelter	956
204	xsun	955	for (i=0; i< nBinsX_; i++) {
205			for(j=0; j< nBinsY_; j++) {
206			newindex = i*nBinsY_ + j;
207			if (gridsample_[newindex] == 0) {
208			// interpolate from surrounding points:
209
210			interpsum = 0.0;
211			ninterp = 0;
212
213			//point1 = bottom;
214
215			px = i;
216			py = j - 1;
217			newp = px*nBinsY_ + py;
218			if ((py >= 0) && (gridsample_[newp] > 0)) {
219			interpsum += gridZ_[newp];
220			ninterp++;
221			}
222
223			//point2 = top;
224
225			px = i;
226			py = j + 1;
227			newp = px*nBinsY_ + py;
228			if ((py < nBinsY_) && (gridsample_[newp] > 0)) {
229			interpsum += gridZ_[newp];
230			ninterp++;
231			}
232
233			//point3 = left;
234
235			px = i - 1;
236			py = j;
237			newp = px*nBinsY_ + py;
238			if ((px >= 0) && (gridsample_[newp] > 0)) {
239			interpsum += gridZ_[newp];
240			ninterp++;
241			}
242
243			//point4 = right;
244
245			px = i + 1;
246			py = j;
247			newp = px*nBinsY_ + py;
248	gezelter	956	if ( (px < nBinsX_ ) && ( gridsample_[newp] > 0 )) {
249			interpsum += gridZ_[newp];
250			ninterp++;
251			}
252
253	xsun	955	value = interpsum / (double)ninterp;
254
255			gridZ_[newindex] = value;
256			}
257			}
258			}
259
260			for (i=0; i < nBinsX_; i++) {
261			for (j=0; j < nBinsY_; j++) {
262			newindex = i*nBinsY_ + j;
263
264			c_re(in[newindex]) = gridZ_[newindex];
265			c_im(in[newindex]) = 0.0;
266			}
267			}
268
269			fftw_execute(p);
270
271			for (i=0; i< nBinsX_; i++) {
272			for(j=0; j< nBinsY_; j++) {
273			newindex = i*nBinsY_ + j;
274			mag[newindex] = pow(c_re(out[newindex]),2) + pow(c_im(out[newindex]),2);
275			}
276			}
277
278			fftw_destroy_plan(p);
279			fftw_free(out);
280			fftw_free(in);
281
282			for (i=0; i< (nBinsX_/2); i++) {
283			for(j=0; j< (nBinsY_/2); j++) {
284			index = i*nBinsY_ + j;
285			new_i = i + (nBinsX_/2);
286			new_j = j + (nBinsY_/2);
287			new_index = new_i*nBinsY_ + new_j;
288			newmag[new_index] = mag[index];
289			}
290			}
291
292			for (i=(nBinsX_/2); i< nBinsX_; i++) {
293			for(j=0; j< (nBinsY_/2); j++) {
294			index = i*nBinsY_ + j;
295			new_i = i - (nBinsX_/2);
296			new_j = j + (nBinsY_/2);
297			new_index = new_i*nBinsY_ + new_j;
298			newmag[new_index] = mag[index];
299			}
300			}
301
302			for (i=0; i< (nBinsX_/2); i++) {
303			for(j=(nBinsY_/2); j< nBinsY_; j++) {
304			index = i*nBinsY_ + j;
305			new_i = i + (nBinsX_/2);
306			new_j = j - (nBinsY_/2);
307			new_index = new_i*nBinsY_ + new_j;
308			newmag[new_index] = mag[index];
309			}
310			}
311
312			for (i=(nBinsX_/2); i< nBinsX_; i++) {
313			for(j=(nBinsY_/2); j< nBinsY_; j++) {
314			index = i*nBinsY_ + j;
315			new_i = i - (nBinsX_/2);
316			new_j = j - (nBinsY_/2);
317			new_index = new_i*nBinsY_ + new_j;
318			newmag[new_index] = mag[index];
319			}
320			}
321
322			maxfreqx = 1.0 / gridX_;
323			maxfreqy = 1.0 / gridY_;
324
325			// printf("%lf\t%lf\t%lf\t%lf\n", dx, dy, maxfreqx, maxfreqy);
326
327			maxfreq = sqrt(maxfreqxmaxfreqx + maxfreqymaxfreqy);
328	gezelter	956	dfreq = maxfreq/(double)(nbins_-1);
329	xsun	955
330			//printf("%lf\n", dfreq);
331
332			zero_freq_x = nBinsX_/2;
333			zero_freq_y = nBinsY_/2;
334
335			for (i=0; i< nBinsX_; i++) {
336			for(j=0; j< nBinsY_; j++) {
337
338			freq_x = (double)(i - zero_freq_x)maxfreqx2 / nBinsX_;
339			freq_y = (double)(j - zero_freq_y)maxfreqy2 / nBinsY_;
340
341			freq = sqrt(freq_xfreq_x + freq_yfreq_y);
342
343			whichbin = (int) (freq / dfreq);
344			newindex = i*nBinsY_ + j;
345			// printf("%d %d %lf %lf\n", whichbin, newindex, freq, dfreq);
346			bin[whichbin][istep] += newmag[newindex];
347			samples[whichbin][istep]++;
348			}
349			}
350
351	gezelter	956	for ( i = 0; i < nbins_; i++) {
352	xsun	955	if ( samples[i][istep] > 0) {
353			bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (double)samples[i][istep]) / (double)nMolecules;
354			}
355			}
356
357			}
358
359	gezelter	956	for (int i = 0; i < nbins_; i++) {
360			for (int j = 0; j < nFrames; j++) {
361	xsun	955	sum_bin[i] += bin[i][j];
362			sum_bin_sq[i] += bin[i][j] * bin[i][j];
363			}
364			avg_bin[i] = sum_bin[i] / (double)nFrames;
365			avg_bin_sq[i] = sum_bin_sq[i] / (double)nFrames;
366	gezelter	956	for (int j = 0; j < nFrames; j++) {
367	xsun	955	errbin_sum[i] += pow((bin[i][j] - avg_bin[i]), 2);
368			errbin_sum_sq[i] += pow((bin[i][j] * bin[i][j] - avg_bin_sq[i]), 2);
369			}
370			errbin[i] = sqrt( errbin_sum[i] / (double)nFrames );
371			errbin_sq[i] = sqrt( errbin_sum_sq[i] / (double)nFrames );
372			}
373	gezelter	956
374			printSpectrum();
375			#else
376			sprintf(painCave.errMsg, "Hxy: FFTW support was not compiled in!\n");
377			painCave.isFatal = 1;
378			simError();
379	xsun	955
380	gezelter	956	#endif
381
382			}
383	xsun	955
384			void Hxy::printSpectrum() {
385			std::ofstream rdfStream(outputFilename_.c_str());
386			if (rdfStream.is_open()) {
387
388	gezelter	956	for (int i = 0; i < nbins_; i++) {
389	xsun	955	if ( avg_bin[i] > 0 ){
390			rdfStream << i*dfreq << "\t"
391			<<pow(avg_bin[i], 2)<<"\t"
392			<<errbin_sq[i]<<"\t"
393			<<avg_bin[i]<<"\t"
394			<<errbin[i]<<"\n";
395			}
396			}
397			} else {
398
399			sprintf(painCave.errMsg, "Hxy: unable to open %s\n", outputFilename_.c_str());
400			painCave.isFatal = 1;
401			simError();
402			}
403
404			rdfStream.close();
405			}
406
407			}