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Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 35 | Line 35
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).                        
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/hydrodynamics/BeadModel.hpp"
44 + #include "types/LennardJonesAdapter.hpp"
45  
46   namespace OpenMD {
47    bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
# Line 74 | Line 76 | namespace OpenMD {
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 = OPENMD_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) {

Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

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