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root/OpenMD/trunk/src/applications/staticProps/RadialDistrFunc.cpp
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Comparing trunk/src/applications/staticProps/RadialDistrFunc.cpp (file contents):
Revision 543 by tim, Thu May 26 22:45:00 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 "RadialDistrFunc.hpp"
45   #include "io/DumpReader.hpp"
46   #include "primitives/Molecule.hpp"
47 < namespace oopse {
47 > namespace OpenMD {
48  
49    RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50      : StaticAnalyser(info, filename),
# Line 131 | Line 131 | namespace oopse {
131        //stage 3 are completely overlapping
132  
133        if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
134 –
134          common_ = seleMan1_ & seleMan2_;
135          sele1_minus_common_ = seleMan1_ - common_;
136          sele2_minus_common_ = seleMan2_ - common_;            
# Line 139 | Line 138 | namespace oopse {
138          int nSelected2 = seleMan2_.getSelectionCount();
139          int nIntersect = common_.getSelectionCount();
140              
141 <        nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;                      
141 >        nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
142        }
144 –
143        processNonOverlapping(sele1_minus_common_, seleMan2_);
144        processNonOverlapping(common_, sele2_minus_common_);        
145        processOverlapping(common_);
146 <        
149 <        
146 >      
147        processHistogram();
148          
149      }

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