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root/OpenMD/trunk/src/UseTheForce/CLAYFF.cpp
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Comparing trunk/src/UseTheForce/CLAYFF.cpp (file contents):
Revision 788 by gezelter, Mon Dec 5 22:23:57 2005 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  
43   #include "UseTheForce/CLAYFF.hpp"
44   #include "UseTheForce/DarkSide/lj_interface.h"
45   #include "UseTheForce/ForceFieldFactory.hpp"
46 + #include "io/BaseAtomTypesSectionParser.hpp"
47   #include "io/AtomTypesSectionParser.hpp"
48   #include "io/LennardJonesAtomTypesSectionParser.hpp"
49   #include "io/ChargeAtomTypesSectionParser.hpp"
# Line 51 | Line 52
52   #include "io/OptionSectionParser.hpp"
53   #include "UseTheForce/ForceFieldCreator.hpp"
54  
55 < namespace oopse {
55 > namespace OpenMD {
56      
57    CLAYFF::CLAYFF(){
58  
# Line 59 | Line 60 | namespace oopse {
60      setForceFieldFileName("CLAYFF.frc");
61  
62      spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
63 +    spMan_.push_back(new BaseAtomTypesSectionParser());
64      spMan_.push_back(new AtomTypesSectionParser());
65 <    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
66 <    spMan_.push_back(new ChargeAtomTypesSectionParser());
67 <    spMan_.push_back(new BondTypesSectionParser());
68 <    spMan_.push_back(new BendTypesSectionParser());
65 >    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
66 >    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
67 >    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
68 >    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
69      
70    }
71  
# Line 78 | Line 80 | namespace oopse {
80  
81      for (at = atomTypeCont_.beginType(i); at != NULL;
82           at = atomTypeCont_.nextType(i)) {
83 +      // useBase sets the responsibilities, and these have to be done
84 +      // after the atomTypes and Base types have all been scanned:
85 +
86 +      std::vector<AtomType*> ayb = at->allYourBase();      
87 +      if (ayb.size() > 1) {
88 +        for (int j = ayb.size()-1; j > 0; j--) {
89 +          
90 +          ayb[j-1]->useBase(ayb[j]);
91 +
92 +        }
93 +      }
94        at->makeFortranAtomType();
95      }
96  
# Line 95 | Line 108 | namespace oopse {
108    CLAYFF::~CLAYFF(){
109      destroyLJTypes();
110    }
111 < } //end namespace oopse
111 > } //end namespace OpenMD

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