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Comparing trunk/src/applications/staticProps/RippleOP.cpp (file contents):
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 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/RippleOP.hpp"
# Line 44 | Line 45
45   #include "io/DumpReader.hpp"
46   #include "primitives/Molecule.hpp"
47   #include "utils/NumericConstant.hpp"
48 < namespace oopse {
48 > #include "types/MultipoleAdapter.hpp"
49 > namespace OpenMD {
50  
51  
52    RippleOP::RippleOP(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
# Line 62 | Line 64 | namespace oopse {
64      }else {
65        sprintf( painCave.errMsg,
66                 "--sele1 must be static selection\n");
67 <      painCave.severity = OOPSE_ERROR;
67 >      painCave.severity = OPENMD_ERROR;
68        painCave.isFatal = 1;
69        simError();  
70      }
# Line 72 | Line 74 | namespace oopse {
74      }else {
75        sprintf( painCave.errMsg,
76                 "--sele2 must be static selection\n");
77 <      painCave.severity = OOPSE_ERROR;
77 >      painCave.severity = OPENMD_ERROR;
78        painCave.isFatal = 1;
79        simError();  
80      }
# Line 80 | Line 82 | namespace oopse {
82      if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
83        sprintf( painCave.errMsg,
84                 "The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
85 <      painCave.severity = OOPSE_ERROR;
85 >      painCave.severity = OPENMD_ERROR;
86        painCave.isFatal = 1;
87        simError();  
88  
# Line 150 | Line 152 | namespace oopse {
152            currentSnapshot_->wrapVector(pos);
153          Vector3d vecHeadUpper;
154          if (pos.z() >= avgZ){
155 <          vecHeadUpper = j1->getElectroFrame().getColumn(2);
155 >          AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();          
156 >          MultipoleAdapter ma1 = MultipoleAdapter(atype1);
157 >          if (ma1.isDipole())
158 >            vecHeadUpper = j1->getDipole();
159 >          else
160 >            vecHeadUpper = j1->getA().transpose()*V3Z;
161            nUpper++;
162          }
163          Vector3d vecHeadLower;
164          if (pos.z() <= avgZ){
165 <          vecHeadLower = j1->getElectroFrame().getColumn(2);
165 >          AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();          
166 >          MultipoleAdapter ma1 = MultipoleAdapter(atype1);
167 >          if (ma1.isDipole())
168 >            vecHeadLower = j1->getDipole();
169 >          else
170 >            vecHeadLower = j1->getA().transpose() * V3Z;
171            nLower++;
172          }
173          orderTensorHeadUpper +=outProduct(vecHeadUpper, vecHeadUpper);

Comparing trunk/src/applications/staticProps/RippleOP.cpp (property svn:keywords):
Revision 1213 by xsun, Wed Jan 23 21:21:50 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 0 | Line 1
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