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Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (file contents):
Revision 898 by tim, Wed Mar 15 15:51:44 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 {
45 < bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
46 <
44 > namespace OpenMD {
45 >  bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
46 >    
47      if (sd_->isAtom()) {
48 <        createSingleBead(static_cast<Atom*>(sd_), beads);
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 = OPENMD_ERROR;
52 >        painCave.isFatal = 1;
53 >        simError();    
54 >        return false;
55 >      }
56      }
57      else if (sd_->isRigidBody()) {
58 <        RigidBody* rb = static_cast<RigidBody*>(sd_);
59 <        std::vector<Atom*>::iterator ai;
60 <        Atom* atom;
61 <        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
62 <            if (!createSingleBead(atom, beads))
63 <                return false;
58 >      RigidBody* rb = static_cast<RigidBody*>(sd_);
59 >      std::vector<Atom*>::iterator ai;
60 >      Atom* atom;
61 >      for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
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 = OPENMD_ERROR;
66 >          painCave.isFatal = 1;
67 >          simError();    
68 >          return false;
69          }
70 <    }
71 <
70 >      }
71 >    }    
72      return true;
73 < }
74 <
75 < bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
73 >  }
74 >  
75 >  bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
76      AtomType* atomType = atom->getAtomType();
77 <
77 >    
78      if (atomType->isGayBerne()) {
79 <        return false;
79 >      return false;
80      } else if (atomType->isLennardJones()){
81 <        GenericData* data = atomType->getPropertyByName("LennardJones");
82 <        if (data != NULL) {
83 <            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
84 <
85 <            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);
81 >      GenericData* data = atomType->getPropertyByName("LennardJones");
82 >      if (data != NULL) {
83 >        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
84 >        
85 >        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 <        }
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 >      }
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      }
117 <
118 <    return true;
117 >    return true;    
118 >  }
119   }
92 –
93 – }

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