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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 507 by gezelter, Fri Apr 15 22:04:00 2005 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 37 | Line 28
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 + * 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   */
41  
42   #include <algorithm>
# Line 44 | Line 44
44   #include "applications/staticProps/GofAngle2.hpp"
45   #include "utils/simError.h"
46  
47 < namespace oopse {
47 > namespace OpenMD {
48  
49    GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
50                         const std::string& sele2, int nangleBins)
# Line 93 | Line 93 | namespace oopse {
93      Vector3d pos1 = sd1->getPos();
94      Vector3d pos2 = sd2->getPos();
95      Vector3d r12 = pos1 - pos2;
96 <    currentSnapshot_->wrapVector(r12);
96 >    if (usePeriodicBoundaryConditions_)
97 >      currentSnapshot_->wrapVector(r12);
98      Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
99      Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
100      
# Line 102 | Line 103 | namespace oopse {
103      dipole2.normalize();    
104      
105  
106 <    double cosAngle1 = dot(r12, dipole1);
107 <    double cosAngle2 = dot(dipole1, dipole2);
106 >    RealType cosAngle1 = dot(r12, dipole1);
107 >    RealType cosAngle2 = dot(dipole1, dipole2);
108  
109 <    double halfBin = (nAngleBins_ - 1) * 0.5;
109 >    RealType halfBin = (nAngleBins_ - 1) * 0.5;
110      int angleBin1 = halfBin * (cosAngle1 + 1.0);
111 <    int angleBin2 = halfBin * (cosAngle1 + 1.0);
111 >    int angleBin2 = halfBin * (cosAngle2 + 1.0);
112  
113 <    ++histogram_[angleBin1][angleBin1];    
113 >    ++histogram_[angleBin1][angleBin2];    
114      ++npairs_;
115    }
116  
# Line 121 | Line 122 | namespace oopse {
122        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
123        rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
124        for (int i = 0; i < avgGofr_.size(); ++i) {
125 <        double cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
125 >        RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
126  
127          for(int j = 0; j < avgGofr_[i].size(); ++j) {
128 <          double cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
128 >          RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
129            rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
130          }
131  

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