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root/OpenMD/branches/heatflux/src/UseTheForce/SHAPES_FF.cpp
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Comparing trunk/src/UseTheForce/SHAPES_FF.cpp (file contents):
Revision 802 by chuckv, Thu Dec 8 15:38:49 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   #include "UseTheForce/DarkSide/shapes_interface.h"
# Line 45 | Line 45
45   #include "UseTheForce/ForceFieldFactory.hpp"
46   #include "io/OptionSectionParser.hpp"
47   #include "io/DirectionalAtomTypesSectionParser.hpp"
48 + #include "io/BaseAtomTypesSectionParser.hpp"
49   #include "io/AtomTypesSectionParser.hpp"
50   #include "io/LennardJonesAtomTypesSectionParser.hpp"
51   #include "io/ChargeAtomTypesSectionParser.hpp"
# Line 57 | Line 58
58   #include "UseTheForce/ForceFieldCreator.hpp"
59   #include "UseTheForce/SHAPES_FF.hpp"
60   #include "utils/simError.h"
61 < namespace oopse {
61 > namespace OpenMD {
62      
63    SHAPES_FF::SHAPES_FF(){
64      
65      //set default force field filename
66      setForceFieldFileName("Shapes.frc");
67      
67 –    //The ordering of section parsers is important...
68 –    //OptionSectionParser must come first to set options for other parsers
69 –    //DirectionalAtomTypesSectionParser should be before
70 –    //AtomTypesSectionParser since these two section parsers will actually
71 –    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType
72 –    //and DirectionalAtomTypesSectionParser will create DirectionalAtomType
73 –    //which is a subclass of AtomType, therefore it should come first). Other
74 –    //AtomTypes Section Parser will not create the "real" AtomType, they only
75 –    //add and set some attribute of the AtomType. Thus the ordering of these
76 –    //are not important. AtomTypesSectionParser should be added before other atom
77 –    //type section parsers. Make sure they are added after
78 –    //DirectionalAtomTypesSectionParser and AtomTypesSectionParser. The order
79 –    //of BondTypesSectionParser, BendTypesSectionParser and
80 –    //TorsionTypesSectionParser are not important.
68      spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
69      spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_));
70 <    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
70 >    spMan_.push_back(new BaseAtomTypesSectionParser());
71      spMan_.push_back(new AtomTypesSectionParser());
72 +    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
73      spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
74      spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
75      spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
# Line 108 | Line 96 | namespace oopse {
96      AtomType* at;
97      
98      for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
99 +      // useBase sets the responsibilities, and these have to be done
100 +      // after the atomTypes and Base types have all been scanned:
101 +
102 +      std::vector<AtomType*> ayb = at->allYourBase();      
103 +      if (ayb.size() > 1) {
104 +        for (int j = ayb.size()-1; j > 0; j--) {
105 +          
106 +          ayb[j-1]->useBase(ayb[j]);
107 +
108 +        }
109 +      }
110        at->makeFortranAtomType();
111      }
112      
# Line 122 | Line 121 | namespace oopse {
121    }
122    
123    
124 < //  double SHAPES_FF::getRcutFromAtomType(AtomType* at){
124 > //  RealType SHAPES_FF::getRcutFromAtomType(AtomType* at){
125   //  }
126 < } //end namespace oopse
126 > } //end namespace OpenMD
127    

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