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. 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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 *
 *
 *  Created by Xiuquan Sun on 05/09/06.
 *  @author  Xiuquan Sun 
 *  @version $Id$
 *
 */

/* 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 OpenMD {
  
  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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	12968 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	xsun	955	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	xsun	955	* 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	gezelter	1390	* 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, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	xsun	955	*
41			*
42			* Created by Xiuquan Sun on 05/09/06.
43			* @author Xiuquan Sun
44	gezelter	1442	* @version $Id$
45	xsun	955	*
46			*/
47
48			/* Calculates the undulation spectrum of the lipid membrance. */
49
50			#include <algorithm>
51			#include <fstream>
52			#include "applications/staticProps/Hxy.hpp"
53			#include "utils/simError.h"
54			#include "io/DumpReader.hpp"
55			#include "primitives/Molecule.hpp"
56			#include<stdio.h>
57			#include<string.h>
58			#include<stdlib.h>
59			#include<math.h>
60
61	gezelter	1390	namespace OpenMD {
62	xsun	955
63			Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins)
64			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){
65
66			evaluator_.loadScriptString(sele);
67			if (!evaluator_.isDynamic()) {
68			seleMan_.setSelectionSet(evaluator_.evaluate());
69			}
70
71			gridsample_.resize(nBinsX_*nBinsY_);
72			gridZ_.resize(nBinsX_*nBinsY_);
73	xsun	967	mag.resize(nBinsX_*nBinsY_);
74			newmag.resize(nBinsX_*nBinsY_);
75	xsun	955
76	gezelter	956	sum_bin.resize(nbins_);
77			avg_bin.resize(nbins_);
78			errbin_sum.resize(nbins_);
79			errbin.resize(nbins_);
80			sum_bin_sq.resize(nbins_);
81			avg_bin_sq.resize(nbins_);
82			errbin_sum_sq.resize(nbins_);
83			errbin_sq.resize(nbins_);
84	xsun	955
85	xsun	967	bin.resize(nbins_);
86			samples.resize(nbins_);
87
88	xsun	955	setOutputName(getPrefix(filename) + ".Hxy");
89			}
90
91	xsun	967	Hxy::~Hxy(){
92			gridsample_.clear();
93			gridZ_.clear();
94			sum_bin.clear();
95			avg_bin.clear();
96			errbin_sum.clear();
97			errbin.clear();
98			sum_bin_sq.clear();
99			avg_bin_sq.clear();
100			errbin_sum_sq.clear();
101			errbin_sq.clear();
102
103			for(int i=0; i < bin.size(); i++)
104			bin[i].clear();
105			for(int i=0; i < samples.size(); i++)
106			samples[i].clear();
107
108			mag.clear();
109			newmag.clear();
110			}
111
112	xsun	955	void Hxy::process() {
113	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
114	xsun	955	DumpReader reader(info_, dumpFilename_);
115			int nFrames = reader.getNFrames();
116			nProcessed_ = nFrames/step_;
117	gezelter	956
118	xsun	967	for(int k=0; k < bin.size(); k++)
119			bin[k].resize(nFrames);
120			for(int k=0; k < samples.size(); k++)
121			samples[k].resize(nFrames);
122
123	tim	963	RealType lenX_, lenY_;
124			RealType gridX_, gridY_;
125			RealType halfBoxX_, halfBoxY_;
126	xsun	967
127	xsun	955	int binNoX, binNoY;
128	tim	963	RealType interpsum, value;
129	xsun	955	int ninterp, px, py, newp;
130			int newx, newy, newindex, index;
131			int new_i, new_j, new_index;
132	xsun	967
133	tim	963	RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq;
134	xsun	967	RealType maxfreqx, maxfreqy, maxfreq;
135
136	xsun	955	int whichbin;
137	gezelter	956	int nMolecules;
138	xsun	967
139	xsun	969	std::fill(sum_bin.begin(), sum_bin.end(), 0.0);
140			std::fill(avg_bin.begin(), avg_bin.end(), 0.0);
141			std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0);
142			std::fill(errbin.begin(), errbin.end(), 0.0);
143			std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0);
144			std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0);
145			std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0);
146			std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0);
147
148			for(int i=0; i < bin.size(); i++)
149			std::fill(bin[i].begin(), bin[i].end(), 0.0);
150
151			for(int i=0; i < samples.size(); i++)
152			std::fill(samples[i].begin(), samples[i].end(), 0);
153
154	xsun	955	for (int istep = 0; istep < nFrames; istep += step_) {
155
156	gezelter	956	reader.readFrame(istep);
157			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
158			nMolecules = info_->getNGlobalMolecules();
159	gezelter	957
160	gezelter	956	Mat3x3d hmat = currentSnapshot_->getHmat();
161
162	gezelter	957	#ifdef HAVE_FFTW3_H
163			fftw_plan p;
164			#else
165			fftwnd_plan p;
166			#endif
167	xsun	955	fftw_complex in, out;
168	gezelter	956
169			in = (fftw_complex) fftw_malloc(sizeof(fftw_complex) (nBinsX_*nBinsY_));
170			out = (fftw_complex) fftw_malloc(sizeof(fftw_complex) (nBinsX_*nBinsY_));
171	gezelter	957
172			#ifdef HAVE_FFTW3_H
173			p = fftw_plan_dft_2d(nBinsX_, nBinsY_, in, out,
174			FFTW_FORWARD, FFTW_ESTIMATE);
175			#else
176			p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE);
177			#endif
178	xsun	969
179	xsun	967	std::fill(gridsample_.begin(), gridsample_.end(), 0);
180			std::fill(gridZ_.begin(), gridZ_.end(), 0.0);
181			std::fill(mag.begin(), mag.end(), 0.0);
182			std::fill(newmag.begin(), newmag.end(), 0.0);
183
184	xsun	969	int i, j;
185	gezelter	956
186	xsun	955	StuntDouble* sd;
187	gezelter	956
188	xsun	955	lenX_ = hmat(0,0);
189			lenY_ = hmat(1,1);
190	gezelter	956
191	xsun	955	gridX_ = lenX_ /(nBinsX_);
192			gridY_ = lenY_ /(nBinsY_);
193	gezelter	956
194	xsun	967	halfBoxX_ = lenX_ / 2.0;
195			halfBoxY_ = lenY_ / 2.0;
196	gezelter	956
197	xsun	955	if (evaluator_.isDynamic()) {
198			seleMan_.setSelectionSet(evaluator_.evaluate());
199			}
200
201			//wrap the stuntdoubles into a cell
202			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
203			Vector3d pos = sd->getPos();
204	gezelter	1078	if (usePeriodicBoundaryConditions_)
205			currentSnapshot_->wrapVector(pos);
206	xsun	955	sd->setPos(pos);
207	xsun	967	}
208	xsun	955
209			//determine which atom belongs to which grid
210			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
211			Vector3d pos = sd->getPos();
212			//int binNo = (pos.z() /deltaR_) - 1;
213	xsun	967	int binNoX = (int) ((pos.x() + halfBoxX_) / gridX_);
214			int binNoY = (int) ((pos.y() + halfBoxY_) / gridY_);
215	xsun	955	//std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = " << deltaR_ << " binNo = " << binNo << "\n";
216			gridZ_[binNoX*nBinsY_+binNoY] += pos.z();
217			gridsample_[binNoX*nBinsY_+binNoY]++;
218			}
219
220			// FFT stuff depends on nx and ny, so delay allocation until we have
221			// that information
222
223			for(i = 0; i < nBinsX_; i++){
224			for(j = 0; j < nBinsY_; j++){
225			newindex = i * nBinsY_ + j;
226			if(gridsample_[newindex] > 0){
227	tim	963	gridZ_[newindex] = gridZ_[newindex] / (RealType)gridsample_[newindex];
228	xsun	955	}
229			}
230			}
231	gezelter	956
232	xsun	955	for (i=0; i< nBinsX_; i++) {
233			for(j=0; j< nBinsY_; j++) {
234			newindex = i*nBinsY_ + j;
235			if (gridsample_[newindex] == 0) {
236			// interpolate from surrounding points:
237
238			interpsum = 0.0;
239			ninterp = 0;
240
241			//point1 = bottom;
242
243			px = i;
244			py = j - 1;
245			newp = px*nBinsY_ + py;
246			if ((py >= 0) && (gridsample_[newp] > 0)) {
247			interpsum += gridZ_[newp];
248			ninterp++;
249			}
250
251			//point2 = top;
252
253			px = i;
254			py = j + 1;
255			newp = px*nBinsY_ + py;
256			if ((py < nBinsY_) && (gridsample_[newp] > 0)) {
257			interpsum += gridZ_[newp];
258			ninterp++;
259			}
260
261			//point3 = left;
262
263			px = i - 1;
264			py = j;
265			newp = px*nBinsY_ + py;
266			if ((px >= 0) && (gridsample_[newp] > 0)) {
267			interpsum += gridZ_[newp];
268			ninterp++;
269			}
270
271			//point4 = right;
272
273			px = i + 1;
274			py = j;
275			newp = px*nBinsY_ + py;
276	gezelter	956	if ( (px < nBinsX_ ) && ( gridsample_[newp] > 0 )) {
277			interpsum += gridZ_[newp];
278			ninterp++;
279			}
280
281	tim	963	value = interpsum / (RealType)ninterp;
282	xsun	955
283			gridZ_[newindex] = value;
284			}
285			}
286			}
287
288			for (i=0; i < nBinsX_; i++) {
289			for (j=0; j < nBinsY_; j++) {
290			newindex = i*nBinsY_ + j;
291
292			c_re(in[newindex]) = gridZ_[newindex];
293			c_im(in[newindex]) = 0.0;
294			}
295			}
296	xsun	967
297	gezelter	957	#ifdef HAVE_FFTW3_H
298			fftw_execute(p);
299			#else
300			fftwnd_one(p, in, out);
301			#endif
302	xsun	955
303			for (i=0; i< nBinsX_; i++) {
304			for(j=0; j< nBinsY_; j++) {
305			newindex = i*nBinsY_ + j;
306			mag[newindex] = pow(c_re(out[newindex]),2) + pow(c_im(out[newindex]),2);
307			}
308			}
309	xsun	967
310	gezelter	957	#ifdef HAVE_FFTW3_H
311	xsun	955	fftw_destroy_plan(p);
312	gezelter	957	#else
313			fftwnd_destroy_plan(p);
314			#endif
315	xsun	955	fftw_free(out);
316			fftw_free(in);
317
318			for (i=0; i< (nBinsX_/2); i++) {
319			for(j=0; j< (nBinsY_/2); j++) {
320			index = i*nBinsY_ + j;
321			new_i = i + (nBinsX_/2);
322			new_j = j + (nBinsY_/2);
323			new_index = new_i*nBinsY_ + new_j;
324			newmag[new_index] = mag[index];
325			}
326			}
327
328			for (i=(nBinsX_/2); i< nBinsX_; i++) {
329			for(j=0; j< (nBinsY_/2); j++) {
330			index = i*nBinsY_ + j;
331			new_i = i - (nBinsX_/2);
332			new_j = j + (nBinsY_/2);
333			new_index = new_i*nBinsY_ + new_j;
334			newmag[new_index] = mag[index];
335			}
336			}
337
338			for (i=0; i< (nBinsX_/2); i++) {
339			for(j=(nBinsY_/2); j< nBinsY_; j++) {
340			index = i*nBinsY_ + j;
341			new_i = i + (nBinsX_/2);
342			new_j = j - (nBinsY_/2);
343			new_index = new_i*nBinsY_ + new_j;
344			newmag[new_index] = mag[index];
345			}
346			}
347
348			for (i=(nBinsX_/2); i< nBinsX_; i++) {
349			for(j=(nBinsY_/2); j< nBinsY_; j++) {
350			index = i*nBinsY_ + j;
351			new_i = i - (nBinsX_/2);
352			new_j = j - (nBinsY_/2);
353			new_index = new_i*nBinsY_ + new_j;
354			newmag[new_index] = mag[index];
355			}
356			}
357
358			maxfreqx = 1.0 / gridX_;
359			maxfreqy = 1.0 / gridY_;
360
361			// printf("%lf\t%lf\t%lf\t%lf\n", dx, dy, maxfreqx, maxfreqy);
362
363			maxfreq = sqrt(maxfreqxmaxfreqx + maxfreqymaxfreqy);
364	tim	963	dfreq = maxfreq/(RealType)(nbins_-1);
365	xsun	955
366			//printf("%lf\n", dfreq);
367
368			zero_freq_x = nBinsX_/2;
369			zero_freq_y = nBinsY_/2;
370
371			for (i=0; i< nBinsX_; i++) {
372			for(j=0; j< nBinsY_; j++) {
373
374	tim	963	freq_x = (RealType)(i - zero_freq_x)maxfreqx2 / nBinsX_;
375			freq_y = (RealType)(j - zero_freq_y)maxfreqy2 / nBinsY_;
376	xsun	955
377			freq = sqrt(freq_xfreq_x + freq_yfreq_y);
378
379			whichbin = (int) (freq / dfreq);
380			newindex = i*nBinsY_ + j;
381			// printf("%d %d %lf %lf\n", whichbin, newindex, freq, dfreq);
382			bin[whichbin][istep] += newmag[newindex];
383			samples[whichbin][istep]++;
384			}
385			}
386
387	gezelter	956	for ( i = 0; i < nbins_; i++) {
388	xsun	955	if ( samples[i][istep] > 0) {
389	xsun	969	bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_;
390	xsun	955	}
391			}
392			}
393	xsun	967
394	gezelter	956	for (int i = 0; i < nbins_; i++) {
395			for (int j = 0; j < nFrames; j++) {
396	xsun	955	sum_bin[i] += bin[i][j];
397			sum_bin_sq[i] += bin[i][j] * bin[i][j];
398			}
399	tim	963	avg_bin[i] = sum_bin[i] / (RealType)nFrames;
400			avg_bin_sq[i] = sum_bin_sq[i] / (RealType)nFrames;
401	gezelter	956	for (int j = 0; j < nFrames; j++) {
402	xsun	955	errbin_sum[i] += pow((bin[i][j] - avg_bin[i]), 2);
403			errbin_sum_sq[i] += pow((bin[i][j] * bin[i][j] - avg_bin_sq[i]), 2);
404			}
405	tim	963	errbin[i] = sqrt( errbin_sum[i] / (RealType)nFrames );
406			errbin_sq[i] = sqrt( errbin_sum_sq[i] / (RealType)nFrames );
407	xsun	955	}
408	xsun	967
409	gezelter	956	printSpectrum();
410	xsun	967
411	gezelter	956	#else
412			sprintf(painCave.errMsg, "Hxy: FFTW support was not compiled in!\n");
413			painCave.isFatal = 1;
414			simError();
415	xsun	955
416	gezelter	956	#endif
417	xsun	967	}
418	xsun	955
419			void Hxy::printSpectrum() {
420			std::ofstream rdfStream(outputFilename_.c_str());
421			if (rdfStream.is_open()) {
422	xsun	967
423			for (int i = 0; i < nbins_; ++i) {
424	xsun	955	if ( avg_bin[i] > 0 ){
425	xsun	967	rdfStream << (RealType)i * dfreq << "\t"
426	xsun	955	<<pow(avg_bin[i], 2)<<"\t"
427			<<errbin_sq[i]<<"\t"
428			<<avg_bin[i]<<"\t"
429			<<errbin[i]<<"\n";
430			}
431			}
432			} else {
433
434			sprintf(painCave.errMsg, "Hxy: unable to open %s\n", outputFilename_.c_str());
435			painCave.isFatal = 1;
436			simError();
437			}
438	xsun	967
439	xsun	955	rdfStream.close();
440	xsun	967
441	xsun	955	}
442
443			}