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root/OpenMD/trunk/src/UseTheForce/DUFF.cpp
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Comparing trunk/src/UseTheForce/DUFF.cpp (file contents):
Revision 492 by chuckv, Wed Apr 13 20:36:45 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  
43   #include "UseTheForce/DUFF.hpp"
44   #include "UseTheForce/DarkSide/lj_interface.h"
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"
55   #include "io/StickyAtomTypesSectionParser.hpp"
56 + #include "io/StickyPowerAtomTypesSectionParser.hpp"
57 + #include "io/GayBerneAtomTypesSectionParser.hpp"
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(){
66 >  DUFF::DUFF(){
67  
68      //set default force field filename
69      setForceFieldFileName("DUFF2.frc");
70  
71 <    //the order of adding section parsers are important
72 <    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
67 <    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
68 <    //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
69 <    //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
70 <    //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
71 <    //important. AtomTypesSectionParser should be added before other atom type section parsers.
72 <    //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
73 <    //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
74 <    //not important.
75 <    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 BondTypesSectionParser());
79 <    spMan_.push_back(new BendTypesSectionParser());
80 <    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 < }
85 >  }
86  
87 < void DUFF::parse(const std::string& filename) {
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 93 | Line 95 | void DUFF::parse(const std::string& filename) {
95      ForceField::AtomTypeContainer::MapTypeIterator i;
96      AtomType* at;
97  
98 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
99 <        at->makeFortranAtomType();
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  
114 <    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
115 <        at->complete();
114 >    for (at = atomTypeCont_.beginType(i); at != NULL;
115 >         at = atomTypeCont_.nextType(i)) {
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 < }
134 >  }
135  
136 < DUFF::~DUFF(){
137 <        destroyLJTypes();
138 <        destroyStickyTypes();
139 < }
140 < } //end namespace oopse
136 >  DUFF::~DUFF(){
137 >    destroyLJTypes();
138 >    destroyStickyTypes();
139 >    destroyGayBerneTypes();
140 >  }
141 > } //end namespace OpenMD

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