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root/OpenMD/trunk/src/UseTheForce/DUFF.cpp
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Comparing trunk/src/UseTheForce/DUFF.cpp (file contents):
Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 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  
# Line 47 | Line 47
47   #include "UseTheForce/ForceFieldFactory.hpp"
48   #include "io/BaseAtomTypesSectionParser.hpp"
49   #include "io/DirectionalAtomTypesSectionParser.hpp"
50 – #include "io/BaseAtomTypesSectionParser.hpp"
50   #include "io/AtomTypesSectionParser.hpp"
51   #include "io/BaseAtomTypesSectionParser.hpp"
52   #include "io/LennardJonesAtomTypesSectionParser.hpp"
# Line 62 | Line 61
61   #include "io/OptionSectionParser.hpp"
62   #include "UseTheForce/ForceFieldCreator.hpp"
63  
64 < namespace oopse {
64 > namespace OpenMD {
65      
66    DUFF::DUFF(){
67  
68      //set default force field filename
69      setForceFieldFileName("DUFF2.frc");
70  
72 –    //The order of adding section parsers is important.
73 –    //OptionSectionParser must come first to set options for other parsers
74 –    //DirectionalAtomTypesSectionParser should be added before
75 –    //AtomTypesSectionParser, and these two section parsers will actually
76 –    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
77 –    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
78 –    //is a subclass of AtomType and should come first). Other AtomTypes Section
79 –    //Parser will not create the "real" AtomType, they only add and set some
80 –    //attribute of the AtomType. Thus their order are not important.
81 –    //AtomTypesSectionParser should be added before other atom type section
82 –    //parsers. Make sure they are added after DirectionalAtomTypesSectionParser
83 –    //and AtomTypesSectionParser. The order of BondTypesSectionParser,
84 –    //BendTypesSectionParser and TorsionTypesSectionParser are not important.
71      spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
86 –    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
72      spMan_.push_back(new BaseAtomTypesSectionParser());
73      spMan_.push_back(new AtomTypesSectionParser());
74 +    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
75      spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
76      spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
77      spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
# Line 111 | Line 97 | namespace oopse {
97  
98      for (at = atomTypeCont_.beginType(i); at != NULL;
99           at = atomTypeCont_.nextType(i)) {
100 +      // useBase sets the responsibilities, and these have to be done
101 +      // after the atomTypes and Base types have all been scanned:
102 +
103 +      std::vector<AtomType*> ayb = at->allYourBase();      
104 +      if (ayb.size() > 1) {
105 +        for (int j = ayb.size()-1; j > 0; j--) {
106 +          
107 +          ayb[j-1]->useBase(ayb[j]);
108 +
109 +        }
110 +      }
111        at->makeFortranAtomType();
112      }
113  
# Line 141 | Line 138 | namespace oopse {
138      destroyStickyTypes();
139      destroyGayBerneTypes();
140    }
141 < } //end namespace oopse
141 > } //end namespace OpenMD

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