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 1.7 2006-10-18 21:58:47 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_);
    mag.resize(nBinsX_*nBinsY_);
    newmag.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_);

    bin.resize(nbins_);
    samples.resize(nbins_);

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

  Hxy::~Hxy(){
      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();
      
      for(int i=0; i < bin.size(); i++)
        bin[i].clear();
      for(int i=0; i < samples.size(); i++)
        samples[i].clear();

      mag.clear();
      newmag.clear();
  }

  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_;
    
    for(int k=0; k < bin.size(); k++)
      bin[k].resize(nFrames);
    for(int k=0; k < samples.size(); k++)
      samples[k].resize(nFrames);

    RealType lenX_, lenY_;
    RealType gridX_, gridY_;
    RealType halfBoxX_, halfBoxY_;

    int binNoX, binNoY;
    RealType interpsum, value;
    int ninterp, px, py, newp;
    int newx, newy, newindex, index;
    int new_i, new_j, new_index;

    RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq;
    RealType maxfreqx, maxfreqy, maxfreq;

    int whichbin;
    int nMolecules;

    std::fill(sum_bin.begin(), sum_bin.end(), 0.0);
    std::fill(avg_bin.begin(), avg_bin.end(), 0.0);
    std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0);
    std::fill(errbin.begin(), errbin.end(), 0.0);
    std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0);
    std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0);
    std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0);
    std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0);
    
    for(int i=0; i < bin.size(); i++)
      std::fill(bin[i].begin(), bin[i].end(), 0.0);
    
    for(int i=0; i < samples.size(); i++)
      std::fill(samples[i].begin(), samples[i].end(), 0);
    
    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

      std::fill(gridsample_.begin(), gridsample_.end(), 0);
      std::fill(gridZ_.begin(), gridZ_.end(), 0.0);
      std::fill(mag.begin(), mag.end(), 0.0);
      std::fill(newmag.begin(), newmag.end(), 0.0);

      int i, j;   
      
      StuntDouble* sd;
      
      lenX_ = hmat(0,0);
      lenY_ = hmat(1,1);
      
      gridX_ = lenX_ /(nBinsX_);
      gridY_ = lenY_ /(nBinsY_);
      
      halfBoxX_ = lenX_ / 2.0;      
      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();
        if (usePeriodicBoundaryConditions_)
          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 = (int) ((pos.x() + halfBoxX_) / gridX_);
        int binNoY = (int) ((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;
          if(gridsample_[newindex] > 0){
            gridZ_[newindex] = gridZ_[newindex] / (RealType)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 / (RealType)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/(RealType)(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 = (RealType)(i - zero_freq_x)*maxfreqx*2 / nBinsX_;
          freq_y = (RealType)(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] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_;
        }
      }    
    }

    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] / (RealType)nFrames;
      avg_bin_sq[i] = sum_bin_sq[i] / (RealType)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] / (RealType)nFrames );
      errbin_sq[i] = sqrt( errbin_sum_sq[i] / (RealType)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 << (RealType)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:	3054
Committed:	Wed Oct 18 21:58:48 2006 UTC (17 years, 9 months ago) by gezelter
File size:	13004 byte(s)
Log Message:	fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
#	User	Rev	Content
1	xsun	2751	/*
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	3054	* @version $Id: Hxy.cpp,v 1.7 2006-10-18 21:58:47 gezelter Exp $
48	xsun	2751	*
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	xsun	2763	mag.resize(nBinsX_*nBinsY_);
77			newmag.resize(nBinsX_*nBinsY_);
78	xsun	2751
79	gezelter	2752	sum_bin.resize(nbins_);
80			avg_bin.resize(nbins_);
81			errbin_sum.resize(nbins_);
82			errbin.resize(nbins_);
83			sum_bin_sq.resize(nbins_);
84			avg_bin_sq.resize(nbins_);
85			errbin_sum_sq.resize(nbins_);
86			errbin_sq.resize(nbins_);
87	xsun	2751
88	xsun	2763	bin.resize(nbins_);
89			samples.resize(nbins_);
90
91	xsun	2751	setOutputName(getPrefix(filename) + ".Hxy");
92			}
93
94	xsun	2763	Hxy::~Hxy(){
95			gridsample_.clear();
96			gridZ_.clear();
97			sum_bin.clear();
98			avg_bin.clear();
99			errbin_sum.clear();
100			errbin.clear();
101			sum_bin_sq.clear();
102			avg_bin_sq.clear();
103			errbin_sum_sq.clear();
104			errbin_sq.clear();
105
106			for(int i=0; i < bin.size(); i++)
107			bin[i].clear();
108			for(int i=0; i < samples.size(); i++)
109			samples[i].clear();
110
111			mag.clear();
112			newmag.clear();
113			}
114
115	xsun	2751	void Hxy::process() {
116	gezelter	2753	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
117	xsun	2751	DumpReader reader(info_, dumpFilename_);
118			int nFrames = reader.getNFrames();
119			nProcessed_ = nFrames/step_;
120	gezelter	2752
121	xsun	2763	for(int k=0; k < bin.size(); k++)
122			bin[k].resize(nFrames);
123			for(int k=0; k < samples.size(); k++)
124			samples[k].resize(nFrames);
125
126	tim	2759	RealType lenX_, lenY_;
127			RealType gridX_, gridY_;
128			RealType halfBoxX_, halfBoxY_;
129	xsun	2763
130	xsun	2751	int binNoX, binNoY;
131	tim	2759	RealType interpsum, value;
132	xsun	2751	int ninterp, px, py, newp;
133			int newx, newy, newindex, index;
134			int new_i, new_j, new_index;
135	xsun	2763
136	tim	2759	RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq;
137	xsun	2763	RealType maxfreqx, maxfreqy, maxfreq;
138
139	xsun	2751	int whichbin;
140	gezelter	2752	int nMolecules;
141	xsun	2763
142	xsun	2765	std::fill(sum_bin.begin(), sum_bin.end(), 0.0);
143			std::fill(avg_bin.begin(), avg_bin.end(), 0.0);
144			std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0);
145			std::fill(errbin.begin(), errbin.end(), 0.0);
146			std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0);
147			std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0);
148			std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0);
149			std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0);
150
151			for(int i=0; i < bin.size(); i++)
152			std::fill(bin[i].begin(), bin[i].end(), 0.0);
153
154			for(int i=0; i < samples.size(); i++)
155			std::fill(samples[i].begin(), samples[i].end(), 0);
156
157	xsun	2751	for (int istep = 0; istep < nFrames; istep += step_) {
158
159	gezelter	2752	reader.readFrame(istep);
160			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
161			nMolecules = info_->getNGlobalMolecules();
162	gezelter	2753
163	gezelter	2752	Mat3x3d hmat = currentSnapshot_->getHmat();
164
165	gezelter	2753	#ifdef HAVE_FFTW3_H
166			fftw_plan p;
167			#else
168			fftwnd_plan p;
169			#endif
170	xsun	2751	fftw_complex in, out;
171	gezelter	2752
172			in = (fftw_complex) fftw_malloc(sizeof(fftw_complex) (nBinsX_*nBinsY_));
173			out = (fftw_complex) fftw_malloc(sizeof(fftw_complex) (nBinsX_*nBinsY_));
174	gezelter	2753
175			#ifdef HAVE_FFTW3_H
176			p = fftw_plan_dft_2d(nBinsX_, nBinsY_, in, out,
177			FFTW_FORWARD, FFTW_ESTIMATE);
178			#else
179			p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE);
180			#endif
181	xsun	2765
182	xsun	2763	std::fill(gridsample_.begin(), gridsample_.end(), 0);
183			std::fill(gridZ_.begin(), gridZ_.end(), 0.0);
184			std::fill(mag.begin(), mag.end(), 0.0);
185			std::fill(newmag.begin(), newmag.end(), 0.0);
186
187	xsun	2765	int i, j;
188	gezelter	2752
189	xsun	2751	StuntDouble* sd;
190	gezelter	2752
191	xsun	2751	lenX_ = hmat(0,0);
192			lenY_ = hmat(1,1);
193	gezelter	2752
194	xsun	2751	gridX_ = lenX_ /(nBinsX_);
195			gridY_ = lenY_ /(nBinsY_);
196	gezelter	2752
197	xsun	2763	halfBoxX_ = lenX_ / 2.0;
198			halfBoxY_ = lenY_ / 2.0;
199	gezelter	2752
200	xsun	2751	if (evaluator_.isDynamic()) {
201			seleMan_.setSelectionSet(evaluator_.evaluate());
202			}
203
204			//wrap the stuntdoubles into a cell
205			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
206			Vector3d pos = sd->getPos();
207	gezelter	3054	if (usePeriodicBoundaryConditions_)
208			currentSnapshot_->wrapVector(pos);
209	xsun	2751	sd->setPos(pos);
210	xsun	2763	}
211	xsun	2751
212			//determine which atom belongs to which grid
213			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
214			Vector3d pos = sd->getPos();
215			//int binNo = (pos.z() /deltaR_) - 1;
216	xsun	2763	int binNoX = (int) ((pos.x() + halfBoxX_) / gridX_);
217			int binNoY = (int) ((pos.y() + halfBoxY_) / gridY_);
218	xsun	2751	//std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = " << deltaR_ << " binNo = " << binNo << "\n";
219			gridZ_[binNoX*nBinsY_+binNoY] += pos.z();
220			gridsample_[binNoX*nBinsY_+binNoY]++;
221			}
222
223			// FFT stuff depends on nx and ny, so delay allocation until we have
224			// that information
225
226			for(i = 0; i < nBinsX_; i++){
227			for(j = 0; j < nBinsY_; j++){
228			newindex = i * nBinsY_ + j;
229			if(gridsample_[newindex] > 0){
230	tim	2759	gridZ_[newindex] = gridZ_[newindex] / (RealType)gridsample_[newindex];
231	xsun	2751	}
232			}
233			}
234	gezelter	2752
235	xsun	2751	for (i=0; i< nBinsX_; i++) {
236			for(j=0; j< nBinsY_; j++) {
237			newindex = i*nBinsY_ + j;
238			if (gridsample_[newindex] == 0) {
239			// interpolate from surrounding points:
240
241			interpsum = 0.0;
242			ninterp = 0;
243
244			//point1 = bottom;
245
246			px = i;
247			py = j - 1;
248			newp = px*nBinsY_ + py;
249			if ((py >= 0) && (gridsample_[newp] > 0)) {
250			interpsum += gridZ_[newp];
251			ninterp++;
252			}
253
254			//point2 = top;
255
256			px = i;
257			py = j + 1;
258			newp = px*nBinsY_ + py;
259			if ((py < nBinsY_) && (gridsample_[newp] > 0)) {
260			interpsum += gridZ_[newp];
261			ninterp++;
262			}
263
264			//point3 = left;
265
266			px = i - 1;
267			py = j;
268			newp = px*nBinsY_ + py;
269			if ((px >= 0) && (gridsample_[newp] > 0)) {
270			interpsum += gridZ_[newp];
271			ninterp++;
272			}
273
274			//point4 = right;
275
276			px = i + 1;
277			py = j;
278			newp = px*nBinsY_ + py;
279	gezelter	2752	if ( (px < nBinsX_ ) && ( gridsample_[newp] > 0 )) {
280			interpsum += gridZ_[newp];
281			ninterp++;
282			}
283
284	tim	2759	value = interpsum / (RealType)ninterp;
285	xsun	2751
286			gridZ_[newindex] = value;
287			}
288			}
289			}
290
291			for (i=0; i < nBinsX_; i++) {
292			for (j=0; j < nBinsY_; j++) {
293			newindex = i*nBinsY_ + j;
294
295			c_re(in[newindex]) = gridZ_[newindex];
296			c_im(in[newindex]) = 0.0;
297			}
298			}
299	xsun	2763
300	gezelter	2753	#ifdef HAVE_FFTW3_H
301			fftw_execute(p);
302			#else
303			fftwnd_one(p, in, out);
304			#endif
305	xsun	2751
306			for (i=0; i< nBinsX_; i++) {
307			for(j=0; j< nBinsY_; j++) {
308			newindex = i*nBinsY_ + j;
309			mag[newindex] = pow(c_re(out[newindex]),2) + pow(c_im(out[newindex]),2);
310			}
311			}
312	xsun	2763
313	gezelter	2753	#ifdef HAVE_FFTW3_H
314	xsun	2751	fftw_destroy_plan(p);
315	gezelter	2753	#else
316			fftwnd_destroy_plan(p);
317			#endif
318	xsun	2751	fftw_free(out);
319			fftw_free(in);
320
321			for (i=0; i< (nBinsX_/2); i++) {
322			for(j=0; j< (nBinsY_/2); j++) {
323			index = i*nBinsY_ + j;
324			new_i = i + (nBinsX_/2);
325			new_j = j + (nBinsY_/2);
326			new_index = new_i*nBinsY_ + new_j;
327			newmag[new_index] = mag[index];
328			}
329			}
330
331			for (i=(nBinsX_/2); i< nBinsX_; i++) {
332			for(j=0; j< (nBinsY_/2); j++) {
333			index = i*nBinsY_ + j;
334			new_i = i - (nBinsX_/2);
335			new_j = j + (nBinsY_/2);
336			new_index = new_i*nBinsY_ + new_j;
337			newmag[new_index] = mag[index];
338			}
339			}
340
341			for (i=0; i< (nBinsX_/2); i++) {
342			for(j=(nBinsY_/2); j< nBinsY_; j++) {
343			index = i*nBinsY_ + j;
344			new_i = i + (nBinsX_/2);
345			new_j = j - (nBinsY_/2);
346			new_index = new_i*nBinsY_ + new_j;
347			newmag[new_index] = mag[index];
348			}
349			}
350
351			for (i=(nBinsX_/2); i< nBinsX_; i++) {
352			for(j=(nBinsY_/2); j< nBinsY_; j++) {
353			index = i*nBinsY_ + j;
354			new_i = i - (nBinsX_/2);
355			new_j = j - (nBinsY_/2);
356			new_index = new_i*nBinsY_ + new_j;
357			newmag[new_index] = mag[index];
358			}
359			}
360
361			maxfreqx = 1.0 / gridX_;
362			maxfreqy = 1.0 / gridY_;
363
364			// printf("%lf\t%lf\t%lf\t%lf\n", dx, dy, maxfreqx, maxfreqy);
365
366			maxfreq = sqrt(maxfreqxmaxfreqx + maxfreqymaxfreqy);
367	tim	2759	dfreq = maxfreq/(RealType)(nbins_-1);
368	xsun	2751
369			//printf("%lf\n", dfreq);
370
371			zero_freq_x = nBinsX_/2;
372			zero_freq_y = nBinsY_/2;
373
374			for (i=0; i< nBinsX_; i++) {
375			for(j=0; j< nBinsY_; j++) {
376
377	tim	2759	freq_x = (RealType)(i - zero_freq_x)maxfreqx2 / nBinsX_;
378			freq_y = (RealType)(j - zero_freq_y)maxfreqy2 / nBinsY_;
379	xsun	2751
380			freq = sqrt(freq_xfreq_x + freq_yfreq_y);
381
382			whichbin = (int) (freq / dfreq);
383			newindex = i*nBinsY_ + j;
384			// printf("%d %d %lf %lf\n", whichbin, newindex, freq, dfreq);
385			bin[whichbin][istep] += newmag[newindex];
386			samples[whichbin][istep]++;
387			}
388			}
389
390	gezelter	2752	for ( i = 0; i < nbins_; i++) {
391	xsun	2751	if ( samples[i][istep] > 0) {
392	xsun	2765	bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_;
393	xsun	2751	}
394			}
395			}
396	xsun	2763
397	gezelter	2752	for (int i = 0; i < nbins_; i++) {
398			for (int j = 0; j < nFrames; j++) {
399	xsun	2751	sum_bin[i] += bin[i][j];
400			sum_bin_sq[i] += bin[i][j] * bin[i][j];
401			}
402	tim	2759	avg_bin[i] = sum_bin[i] / (RealType)nFrames;
403			avg_bin_sq[i] = sum_bin_sq[i] / (RealType)nFrames;
404	gezelter	2752	for (int j = 0; j < nFrames; j++) {
405	xsun	2751	errbin_sum[i] += pow((bin[i][j] - avg_bin[i]), 2);
406			errbin_sum_sq[i] += pow((bin[i][j] * bin[i][j] - avg_bin_sq[i]), 2);
407			}
408	tim	2759	errbin[i] = sqrt( errbin_sum[i] / (RealType)nFrames );
409			errbin_sq[i] = sqrt( errbin_sum_sq[i] / (RealType)nFrames );
410	xsun	2751	}
411	xsun	2763
412	gezelter	2752	printSpectrum();
413	xsun	2763
414	gezelter	2752	#else
415			sprintf(painCave.errMsg, "Hxy: FFTW support was not compiled in!\n");
416			painCave.isFatal = 1;
417			simError();
418	xsun	2751
419	gezelter	2752	#endif
420	xsun	2763	}
421	xsun	2751
422			void Hxy::printSpectrum() {
423			std::ofstream rdfStream(outputFilename_.c_str());
424			if (rdfStream.is_open()) {
425	xsun	2763
426			for (int i = 0; i < nbins_; ++i) {
427	xsun	2751	if ( avg_bin[i] > 0 ){
428	xsun	2763	rdfStream << (RealType)i * dfreq << "\t"
429	xsun	2751	<<pow(avg_bin[i], 2)<<"\t"
430			<<errbin_sq[i]<<"\t"
431			<<avg_bin[i]<<"\t"
432			<<errbin[i]<<"\n";
433			}
434			}
435			} else {
436
437			sprintf(painCave.errMsg, "Hxy: unable to open %s\n", outputFilename_.c_str());
438			painCave.isFatal = 1;
439			simError();
440			}
441	xsun	2763
442	xsun	2751	rdfStream.close();
443	xsun	2763
444	xsun	2751	}
445
446			}