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Comparing branches/development/src/applications/staticProps/BOPofR.cpp (file contents):
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC vs.
Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41   *  Created by J. Daniel Gezelter on 09/26/06.
# Line 50 | Line 50
50   #include "primitives/Molecule.hpp"
51   #include "utils/NumericConstant.hpp"
52   #include "math/Wigner3jm.hpp"
53 + #include "brains/Thermo.hpp"
54  
55   using namespace MATPACK;
56   namespace OpenMD {
# Line 144 | Line 145 | namespace OpenMD {
145    }
146  
147    
148 <  void BOPofR::initalizeHistogram() {
148 >  void BOPofR::initializeHistogram() {
149          for (int i = 0; i < nBins_; i++){
150                  RCount_[i] = 0;
151                  WofR_[i] = 0;
# Line 166 | Line 167 | namespace OpenMD {
167      RealType costheta;
168      RealType phi;
169      RealType r;
169 –    RealType dist;
170      Vector3d rCOM;
171      RealType distCOM;
172      Vector3d pos;
# Line 176 | Line 176 | namespace OpenMD {
176      std::vector<RealType> q2;
177      std::vector<ComplexType> w;
178      std::vector<ComplexType> w_hat;
179 –    std::map<std::pair<int,int>,ComplexType> QBar;
179      std::vector<RealType> Q2;
180      std::vector<RealType> Q;
181      std::vector<ComplexType> W;
182      std::vector<ComplexType> W_hat;
183 <    int nBonds, Nbonds;
183 >    int nBonds;
184      SphericalHarmonic sphericalHarmonic;
185 <    int i, j;
186 <
185 >    int i;
186 >    
187      DumpReader reader(info_, dumpFilename_);    
188      int nFrames = reader.getNFrames();
189      frameCounter_ = 0;
190  
191 +    Thermo thermo(info_);
192 +
193      q_l.resize(lMax_+1);
194      q2.resize(lMax_+1);
195      w.resize(lMax_+1);
# Line 198 | Line 199 | namespace OpenMD {
199      Q.resize(lMax_+1);
200      W.resize(lMax_+1);
201      W_hat.resize(lMax_+1);
201 –    Nbonds = 0;
202  
203      for (int istep = 0; istep < nFrames; istep += step_) {
204        reader.readFrame(istep);
205        frameCounter_++;
206        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
207 <      CenterOfMass = info_->getCom();
207 >      CenterOfMass = thermo.getCom();
208        if (evaluator_.isDynamic()) {
209          seleMan_.setSelectionSet(evaluator_.evaluate());
210        }
# Line 302 | Line 302 | namespace OpenMD {
302              }
303            }
304            
305 <          w_hat[l] = w[l] / pow(q2[l], 1.5);
305 >          w_hat[l] = w[l] / pow(q2[l], RealType(1.5));
306          }
307  
308          collectHistogram(q_l, w_hat, distCOM);
# Line 320 | Line 320 | namespace OpenMD {
320  
321      if ( distCOM < len_){
322        // Figure out where this distance goes...
323 <      int whichBin = distCOM / deltaR_;
323 >      int whichBin = int(distCOM / deltaR_);
324        RCount_[whichBin]++;
325  
326        if(real(what[6]) < -0.15){                                

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