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Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (file contents):
Revision 946 by gezelter, Tue Apr 25 13:35:42 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 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]  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/hydrodynamics/BeadModel.hpp"
44 + #include "types/LennardJonesAdapter.hpp"
45  
46 < namespace oopse {
46 > namespace OpenMD {
47    bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
48      
49      if (sd_->isAtom()) {
50        if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
51          sprintf( painCave.errMsg,
52                   "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
53 <        painCave.severity = OOPSE_ERROR;
53 >        painCave.severity = OPENMD_ERROR;
54          painCave.isFatal = 1;
55          simError();    
56          return false;
# Line 62 | Line 64 | namespace oopse {
64          if (!createSingleBead(atom, beads)) {
65            sprintf( painCave.errMsg,
66                     "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
67 <          painCave.severity = OOPSE_ERROR;
67 >          painCave.severity = OPENMD_ERROR;
68            painCave.isFatal = 1;
69            simError();    
70            return false;
# Line 74 | Line 76 | namespace oopse {
76    
77    bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
78      AtomType* atomType = atom->getAtomType();
79 <    
79 >    LennardJonesAdapter lja = LennardJonesAdapter(atomType);
80      if (atomType->isGayBerne()) {
81        return false;
82 <    } else if (atomType->isLennardJones()){
83 <      GenericData* data = atomType->getPropertyByName("LennardJones");
84 <      if (data != NULL) {
85 <        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
86 <        
87 <        if (ljData != NULL) {
86 <          LJParam ljParam = ljData->getData();
87 <          BeadParam currBead;
88 <          currBead.atomName = atom->getType();
89 <          currBead.pos = atom->getPos();
90 <          currBead.radius = ljParam.sigma/2.0;
91 <          beads.push_back(currBead);
92 <        } else {
93 <          sprintf( painCave.errMsg,
94 <                   "Can not cast GenericData to LJParam\n");
95 <          painCave.severity = OOPSE_ERROR;
96 <          painCave.isFatal = 1;
97 <          simError();          
98 <        }      
99 <      }
82 >    } else if (lja.isLennardJones()){
83 >      BeadParam currBead;
84 >      currBead.atomName = atom->getType();
85 >      currBead.pos = atom->getPos();
86 >      currBead.radius = lja.getSigma()/2.0;
87 >      beads.push_back(currBead);
88      } else {
89        int obanum = etab.GetAtomicNum((atom->getType()).c_str());
90        if (obanum != 0) {
# Line 109 | Line 97 | namespace oopse {
97        } else {
98          sprintf( painCave.errMsg,
99                   "Could not find atom type in default element.txt\n");
100 <        painCave.severity = OOPSE_ERROR;
100 >        painCave.severity = OPENMD_ERROR;
101          painCave.isFatal = 1;
102          simError();          
103        }

Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (property svn:keywords):
Revision 946 by gezelter, Tue Apr 25 13:35:42 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 0 | Line 1
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