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Comparing trunk/src/applications/staticProps/SCDOrderParameter.cpp (file contents):
Revision 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 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   */
42  
43   #include "applications/staticProps/SCDOrderParameter.hpp"
# Line 44 | Line 45
45   #include "io/DumpReader.hpp"
46   #include "primitives/Molecule.hpp"
47   #include "utils/NumericConstant.hpp"
48 < namespace oopse {
48 > namespace OpenMD {
49  
50    SCDElem::SCDElem(SimInfo* info, const std::string& sele1,
51                     const std::string& sele2, const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){
# Line 67 | Line 68 | namespace oopse {
68      }else {
69        sprintf( painCave.errMsg,
70                 "dynamic selection is not allowed\n");
71 <      painCave.severity = OOPSE_ERROR;
71 >      painCave.severity = OPENMD_ERROR;
72        painCave.isFatal = 1;
73        simError();  
74      }
# Line 77 | Line 78 | namespace oopse {
78      }else {
79        sprintf( painCave.errMsg,
80                 "dynamic selection is not allowed\n");
81 <      painCave.severity = OOPSE_ERROR;
81 >      painCave.severity = OPENMD_ERROR;
82        painCave.isFatal = 1;
83        simError();  
84      }
# Line 87 | Line 88 | namespace oopse {
88      }else {
89        sprintf( painCave.errMsg,
90                 "dynamic selection is not allowed\n");
91 <      painCave.severity = OOPSE_ERROR;
91 >      painCave.severity = OPENMD_ERROR;
92        painCave.isFatal = 1;
93        simError();  
94      }
# Line 99 | Line 100 | namespace oopse {
100      if ( nselected1 != nselected2 || nselected1 != nselected3 ) {
101        sprintf( painCave.errMsg,
102                 "The number of selected Stuntdoubles must be the same\n");
103 <      painCave.severity = OOPSE_ERROR;
103 >      painCave.severity = OPENMD_ERROR;
104        painCave.isFatal = 1;
105        simError();  
106      }
# Line 169 | Line 170 | namespace oopse {
170      assert(beginIndex >=0 && endIndex >=0 && beginIndex <= endIndex - 2);
171      for (int i = beginIndex; i <= endIndex -2 ; ++i) {
172        std::string selectionTemplate = "select " + molname + ".";
173 <      std::string sele1 = selectionTemplate + OOPSE_itoa(i);
174 <      std::string sele2 = selectionTemplate + OOPSE_itoa(i+1);
175 <      std::string sele3 = selectionTemplate + OOPSE_itoa(i+2);
173 >      std::string sele1 = selectionTemplate + OpenMD_itoa(i);
174 >      std::string sele2 = selectionTemplate + OpenMD_itoa(i+1);
175 >      std::string sele3 = selectionTemplate + OpenMD_itoa(i+2);
176          
177        scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
178      }

Comparing trunk/src/applications/staticProps/SCDOrderParameter.cpp (property svn:keywords):
Revision 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 0 | Line 1
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