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Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (file contents):
Revision 944 by gezelter, Tue Apr 25 02:06:12 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/hydrodynamics/BeadModel.hpp"
43  
44 < namespace oopse {
44 > namespace OpenMD {
45    bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
46      
47      if (sd_->isAtom()) {
48        if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
49          sprintf( painCave.errMsg,
50                   "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
51 <        painCave.severity = OOPSE_ERROR;
51 >        painCave.severity = OPENMD_ERROR;
52          painCave.isFatal = 1;
53          simError();    
54          return false;
# Line 62 | Line 62 | namespace oopse {
62          if (!createSingleBead(atom, beads)) {
63            sprintf( painCave.errMsg,
64                     "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
65 <          painCave.severity = OOPSE_ERROR;
65 >          painCave.severity = OPENMD_ERROR;
66            painCave.isFatal = 1;
67            simError();    
68            return false;
# Line 92 | Line 92 | namespace oopse {
92          } else {
93            sprintf( painCave.errMsg,
94                     "Can not cast GenericData to LJParam\n");
95 <          painCave.severity = OOPSE_ERROR;
95 >          painCave.severity = OPENMD_ERROR;
96            painCave.isFatal = 1;
97            simError();          
98          }      
99        }
100 <    } else if (atomType->isEAM()) {
101 <      GenericData* data = atomType->getPropertyByName("EAM");
102 <      if (data != NULL) {
103 <        EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);          
104 <        if (eamData != NULL) {
105 <          EAMParam eamParam = eamData->getData();
106 <          BeadParam currBead;
107 <          currBead.atomName = atom->getType();
108 <          currBead.pos = atom->getPos();
109 <          currBead.radius = eamParam.rcut;
110 <          beads.push_back(currBead);
111 <        } else {
112 <          sprintf( painCave.errMsg,
113 <                   "Can not cast GenericData to EAMParam\n");
114 <          painCave.severity = OOPSE_ERROR;
115 <          painCave.isFatal = 1;
116 <          simError();          
117 <        }      
100 >    } else {
101 >      int obanum = etab.GetAtomicNum((atom->getType()).c_str());
102 >      if (obanum != 0) {
103 >        BeadParam currBead;      
104 >        currBead.atomName = atom->getType();
105 >        currBead.pos = atom->getPos();        
106 >        currBead.radius = etab.GetVdwRad(obanum);
107 >        std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n";
108 >        beads.push_back(currBead);
109 >      } else {
110 >        sprintf( painCave.errMsg,
111 >                 "Could not find atom type in default element.txt\n");
112 >        painCave.severity = OPENMD_ERROR;
113 >        painCave.isFatal = 1;
114 >        simError();          
115        }
116 <      return true;
117 <    }  
116 >    }
117 >    return true;    
118    }
119   }

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