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root/OpenMD/trunk/src/applications/staticProps/AngleR.cpp
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Comparing trunk/src/applications/staticProps/AngleR.cpp (file contents):
Revision 1524 by kstocke1, Fri Nov 19 20:48:18 2010 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /* Calculates Angle(R) for DirectionalAtoms*/
# Line 47 | Line 48
48   #include "utils/NumericConstant.hpp"
49   #include "io/DumpReader.hpp"
50   #include "primitives/Molecule.hpp"
51 + #include "brains/Thermo.hpp"
52   #include <math.h>
53  
54   namespace OpenMD {
# Line 87 | Line 89 | namespace OpenMD {
89        StuntDouble* sd;
90        reader.readFrame(istep);
91        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
92 <      Vector3d CenterOfMass = info_->getCom();      
92 >      Thermo thermo(info_);
93 >      Vector3d CenterOfMass = thermo.getCom();      
94        
95        
96        if (evaluator_.isDynamic()) {
# Line 110 | Line 113 | namespace OpenMD {
113            RealType cosangle = dot(r1, dipole);
114            
115            if (distance < len_) {
116 <            int whichBin = distance / deltaR_;
116 >            int whichBin = int(distance / deltaR_);
117              histogram_[whichBin] += cosangle;
118              count_[whichBin] += 1;
119            }
# Line 128 | Line 131 | namespace OpenMD {
131  
132    void AngleR::processHistogram() {
133  
134 <    for(int i = 0 ; i < histogram_.size(); ++i){
134 >    for(unsigned int i = 0 ; i < histogram_.size(); ++i){
135  
136        if (count_[i] > 0)
137          avgAngleR_[i] += histogram_[i] / count_[i];    
# Line 147 | Line 150 | namespace OpenMD {
150      if (rdfStream.is_open()) {
151        rdfStream << "#radial density function Angle(r)\n";
152        rdfStream << "#r\tcorrValue\n";
153 <      for (int i = 0; i < avgAngleR_.size(); ++i) {
153 >      for (unsigned int i = 0; i < avgAngleR_.size(); ++i) {
154          RealType r = deltaR_ * (i + 0.5);
155          rdfStream << r << "\t" << avgAngleR_[i] << "\n";
156        }

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