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root/OpenMD/trunk/src/UseTheForce/DUFF.cpp
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Comparing trunk/src/UseTheForce/DUFF.cpp (file contents):
Revision 676 by gezelter, Mon Oct 17 19:12:45 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  
# Line 45 | Line 45
45   #include "UseTheForce/DarkSide/sticky_interface.h"
46   #include "UseTheForce/DarkSide/gb_interface.h"
47   #include "UseTheForce/ForceFieldFactory.hpp"
48 + #include "io/BaseAtomTypesSectionParser.hpp"
49   #include "io/DirectionalAtomTypesSectionParser.hpp"
50   #include "io/AtomTypesSectionParser.hpp"
51 + #include "io/BaseAtomTypesSectionParser.hpp"
52   #include "io/LennardJonesAtomTypesSectionParser.hpp"
53   #include "io/ChargeAtomTypesSectionParser.hpp"
54   #include "io/MultipoleAtomTypesSectionParser.hpp"
# Line 56 | Line 58
58   #include "io/BondTypesSectionParser.hpp"
59   #include "io/BendTypesSectionParser.hpp"
60   #include "io/TorsionTypesSectionParser.hpp"
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  
71 <    //The order of adding section parsers is important.
72 <    //DirectionalAtomTypesSectionParser should be added before
70 <    //AtomTypesSectionParser, and these two section parsers will actually
71 <    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
72 <    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
73 <    //is a subclass of AtomType and should come first). Other AtomTypes Section
74 <    //Parser will not create the "real" AtomType, they only add and set some
75 <    //attribute of the AtomType. Thus their order are not important.
76 <    //AtomTypesSectionParser should be added before other atom type section
77 <    //parsers. Make sure they are added after DirectionalAtomTypesSectionParser
78 <    //and AtomTypesSectionParser. The order of BondTypesSectionParser,
79 <    //BendTypesSectionParser and TorsionTypesSectionParser are not important.
80 <    spMan_.push_back(new DirectionalAtomTypesSectionParser());
71 >    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));    
72 >    spMan_.push_back(new BaseAtomTypesSectionParser());
73      spMan_.push_back(new AtomTypesSectionParser());
74 <    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
75 <    spMan_.push_back(new ChargeAtomTypesSectionParser());
76 <    spMan_.push_back(new MultipoleAtomTypesSectionParser());
77 <    spMan_.push_back(new StickyAtomTypesSectionParser());
78 <    spMan_.push_back(new StickyPowerAtomTypesSectionParser());
79 <    spMan_.push_back(new GayBerneAtomTypesSectionParser());
80 <    spMan_.push_back(new BondTypesSectionParser());
81 <    spMan_.push_back(new BendTypesSectionParser());
82 <    spMan_.push_back(new TorsionTypesSectionParser());
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_));
78 >    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
79 >    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
80 >    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
81 >    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
82 >    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
83 >    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
84      
85    }
86  
87    void DUFF::parse(const std::string& filename) {
88      ifstrstream* ffStream;
89 +    bool hasGBtypes;
90 +
91      ffStream = openForceFieldFile(filename);
92  
93      spMan_.parse(*ffStream, *this);
# Line 102 | 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 110 | Line 116 | namespace oopse {
116        at->complete();
117      }
118  
119 +    hasGBtypes = false;
120 +    for (at = atomTypeCont_.beginType(i); at != NULL;
121 +         at = atomTypeCont_.nextType(i)) {
122 +      if (at->isGayBerne())
123 +        hasGBtypes = true;
124 +    }
125 +    
126      int isError = 0;
127  
128 +    if (hasGBtypes) {
129 +      completeGBFF(&isError);
130 +    }
131 +
132      delete ffStream;
133      
134    }
# Line 121 | Line 138 | namespace oopse {
138      destroyStickyTypes();
139      destroyGayBerneTypes();
140    }
141 < } //end namespace oopse
141 > } //end namespace OpenMD

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