ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/applications/staticProps/SCDOrderParameter.cpp
(Generate patch)

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

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines