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root/OpenMD/trunk/src/applications/staticProps/GofAngle2.cpp
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Comparing trunk/src/applications/staticProps/GofAngle2.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 43 | Line 43
43   #include <algorithm>
44   #include <fstream>
45   #include "applications/staticProps/GofAngle2.hpp"
46 + #include "primitives/Atom.hpp"
47 + #include "types/MultipoleAdapter.hpp"
48   #include "utils/simError.h"
49  
50   namespace OpenMD {
# Line 72 | Line 74 | namespace OpenMD {
74      }
75    }
76  
77 <  void GofAngle2::initalizeHistogram() {
77 >  void GofAngle2::initializeHistogram() {
78      npairs_ = 0;
79      for (unsigned int i = 0; i < histogram_.size(); ++i)
80        std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
# Line 96 | Line 98 | namespace OpenMD {
98      Vector3d r12 = pos1 - pos2;
99      if (usePeriodicBoundaryConditions_)
100        currentSnapshot_->wrapVector(r12);
101 <    Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
102 <    Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
101 >
102 >    AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
103 >    AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
104 >    MultipoleAdapter ma1 = MultipoleAdapter(atype1);
105 >    MultipoleAdapter ma2 = MultipoleAdapter(atype2);
106 >
107 >    Vector3d dipole1, dipole2;
108 >    if (ma1.isDipole())        
109 >        dipole1 = sd1->getDipole();
110 >    else
111 >        dipole1 = sd1->getA().transpose() * V3Z;
112 >
113 >    if (ma2.isDipole())        
114 >        dipole2 = sd2->getDipole();
115 >    else
116 >        dipole2 = sd2->getA().transpose() * V3Z;
117      
118      r12.normalize();
119      dipole1.normalize();    
# Line 108 | Line 124 | namespace OpenMD {
124      RealType cosAngle2 = dot(dipole1, dipole2);
125  
126      RealType halfBin = (nAngleBins_ - 1) * 0.5;
127 <    int angleBin1 = halfBin * (cosAngle1 + 1.0);
128 <    int angleBin2 = halfBin * (cosAngle2 + 1.0);
127 >    int angleBin1 = int(halfBin * (cosAngle1 + 1.0));
128 >    int angleBin2 = int(halfBin * (cosAngle2 + 1.0));
129  
130      ++histogram_[angleBin1][angleBin2];    
131      ++npairs_;
# Line 123 | Line 139 | namespace OpenMD {
139        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
140        rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
141        for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
142 <        RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
143 <
142 >        // RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
143 >        
144          for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
145 <          RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
145 >          // RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
146            rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
147          }
148  

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