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Comparing trunk/src/brains/Register.cpp (file contents):
Revision 1032 by gezelter, Fri Sep 1 19:16:02 2006 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 "brains/Register.hpp"
# Line 53 | Line 53
53   #include "integrators/NPrT.hpp"
54   #include "integrators/NgammaT.hpp"
55   #include "integrators/LangevinDynamics.hpp"
56 + #if defined(HAVE_QHULL)
57 + #include "integrators/SMIPDynamics.hpp"
58 + #endif
59  
60   #include "minimizers/MinimizerFactory.hpp"
61   #include "minimizers/MinimizerCreator.hpp"
# Line 64 | Line 67
67   #include "UseTheForce/ForceFieldCreator.hpp"
68   #include "UseTheForce/SHAPES_FF.hpp"
69   #include "UseTheForce/SC_FF.hpp"
70 + #include "UseTheForce/MnM_FF.hpp"
71   #include "UseTheForce/CLAYFF.hpp"
72 + #include "UseTheForce/Amber_FF.hpp"
73   #include "lattice/LatticeFactory.hpp"
74   #include "lattice/LatticeCreator.hpp"
75   #include "lattice/FCCLattice.hpp"
76  
77 < //#include "openbabel/amberformat.hpp"
73 < //#include "openbabel/fingerprintformat.hpp"
74 < //#include "openbabel/gromos96format.hpp"
75 < #include "openbabel/oopseformat.hpp"
76 < #include "openbabel/pdbformat.hpp"
77 < //#include "openbabel/povrayformat.hpp"
78 < //#include "openbabel/smilesformat.hpp"
79 < #include "openbabel/tinkerformat.hpp"
80 < #include "openbabel/xyzformat.hpp"
77 > namespace OpenMD {
78  
79  
83 – namespace oopse {
84 –
85 –
80    void registerForceFields() {
81      /** @todo move to a seperate initialization module */
82      //DUFF, WATER and LJ are merged into one force field
# Line 95 | Line 89 | namespace oopse {
89      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SHAPES_FF>("SHAPES"));
90      //Well if EAM worked... then Sutton-Chen should work like a CHARMM(Hopefully not).
91      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SC_FF>("SC"));
92 +    //Well if Sutton-Chen worked... then lets just mangle all of the forcefields together in MnM.
93 +    //That sounds like a good idea right......
94 +    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<MnM_FF>("MnM"));
95      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<CLAYFF>("CLAY"));
96 +    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<Amber_FF>("Amber"));
97    }
98 <
98 >  
99    void registerIntegrators() {
100      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVE>("NVE"));
101      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVT>("NVT"));
# Line 111 | Line 109 | namespace oopse {
109      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGAMMAT"));
110      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LANGEVINDYNAMICS"));
111      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LD"));
112 <    
113 <
112 > #if defined(HAVE_QHULL)
113 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<SMIPDynamics>("SMIPD"));
114 > #endif
115    }
116  
117    void registerMinimizers() {
# Line 124 | Line 123 | namespace oopse {
123      LatticeFactory::getInstance()->registerLattice(new LatticeBuilder<FCCLattice>("FCC"));
124    }
125  
127 –  void registerOBFormats(){
128 –    //static OpenBabel::AmberPrepFormat amberFormatInstance;
129 –    //static OpenBabel::FingerprintFormat fingerprintFormatInstance;
130 –    static OpenBabel::OOPSEFormat oopseFormatInstance;    
131 –    static OpenBabel::PDBFormat pdbFormatInstance;
132 –    //static OpenBabel::PovrayFormat povaryFormatInstance;
133 –    //static OpenBabel::SMIFormat smilesFormatInstance;
134 –    static OpenBabel::TinkerFormat tinkerFormatInstance;
135 –    static OpenBabel::XYZFormat xyzFormatInstance;    
136 –  }
137 –  
126    void registerAll() {
127      registerForceFields();
128      registerIntegrators();

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