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Comparing trunk/src/applications/staticProps/Hxy.cpp (file contents):
Revision 967 by xsun, Mon May 22 15:30:42 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 38 | Line 29
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31   *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   *
42 – *  Hxy.cpp
43 – *  OOPSE-2.0
41   *
42   *  Created by Xiuquan Sun on 05/09/06.
43   *  @author  Xiuquan Sun
44 < *  @version $Id: Hxy.cpp,v 1.5 2006-05-22 15:30:42 xsun Exp $
44 > *  @version $Id: Hxy.cpp,v 1.8 2009-11-25 20:01:59 gezelter Exp $
45   *
46   */
47  
# Line 61 | Line 58
58   #include<stdlib.h>
59   #include<math.h>
60  
61 < namespace oopse {
61 > namespace OpenMD {
62    
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){
# Line 139 | Line 136 | namespace oopse {
136      int whichbin;
137      int nMolecules;
138  
139 +    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      for (int istep = 0; istep < nFrames; istep += step_) {
155        
156        reader.readFrame(istep);
# Line 163 | Line 175 | namespace oopse {
175   #else
176        p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE);
177   #endif
178 <      
167 <      int i, j;  
168 <      
178 >
179        std::fill(gridsample_.begin(), gridsample_.end(), 0);
180        std::fill(gridZ_.begin(), gridZ_.end(), 0.0);
171 –      std::fill(sum_bin.begin(), sum_bin.end(), 0.0);
172 –      std::fill(avg_bin.begin(), avg_bin.end(), 0.0);
173 –      std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0);
174 –      std::fill(errbin.begin(), errbin.end(), 0.0);
175 –      std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0);
176 –      std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0);
177 –      std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0);
178 –      std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0);
181        std::fill(mag.begin(), mag.end(), 0.0);
182        std::fill(newmag.begin(), newmag.end(), 0.0);
183  
184 <      for(i=0; i < bin.size(); i++)
183 <        std::fill(bin[i].begin(), bin[i].end(), 0.0);
184 <
185 <      for(i=0; i < samples.size(); i++)
186 <        std::fill(samples[i].begin(), samples[i].end(), 0);
184 >      int i, j;  
185        
186        StuntDouble* sd;
187        
# Line 203 | Line 201 | namespace oopse {
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 <        currentSnapshot_->wrapVector(pos);
204 >        if (usePeriodicBoundaryConditions_)
205 >          currentSnapshot_->wrapVector(pos);
206          sd->setPos(pos);
207        }
208        
# Line 387 | Line 386 | namespace oopse {
386        
387        for ( i = 0; i < nbins_; i++) {
388          if ( samples[i][istep] > 0) {
389 <          bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nMolecules;
389 >          bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_;
390          }
391        }    
392      }

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