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Comparing:
trunk/src/brains/Register.cpp (file contents), Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
branches/development/src/brains/Register.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "brains/Register.hpp"
# Line 49 | Line 50
50   #include "integrators/NPTi.hpp"
51   #include "integrators/NPTf.hpp"
52   #include "integrators/NPTxyz.hpp"
53 + #include "integrators/NPTsz.hpp"
54   #include "integrators/NPAT.hpp"
55   #include "integrators/NPrT.hpp"
56 + #include "integrators/NgammaT.hpp"
57   #include "integrators/LangevinDynamics.hpp"
58 + #if defined(HAVE_QHULL)
59 + #include "integrators/LangevinHullDynamics.hpp"
60 + #endif
61  
62   #include "minimizers/MinimizerFactory.hpp"
63   #include "minimizers/MinimizerCreator.hpp"
# Line 59 | Line 65
65   #include "minimizers/SDMinimizer.hpp"
66   #include "UseTheForce/DUFF.hpp"
67   #include "UseTheForce/EAM_FF.hpp"
68 + #include "UseTheForce/EADM_FF.hpp"
69   #include "UseTheForce/ForceFieldFactory.hpp"
70   #include "UseTheForce/ForceFieldCreator.hpp"
71   #include "UseTheForce/SHAPES_FF.hpp"
72   #include "UseTheForce/SC_FF.hpp"
73 + #include "UseTheForce/MnM_FF.hpp"
74   #include "UseTheForce/CLAYFF.hpp"
75 + #include "UseTheForce/Amber_FF.hpp"
76   #include "lattice/LatticeFactory.hpp"
77   #include "lattice/LatticeCreator.hpp"
78   #include "lattice/FCCLattice.hpp"
79  
80 < #include "openbabel/amberformat.hpp"
72 < #include "openbabel/fingerprintformat.hpp"
73 < #include "openbabel/gromos96format.hpp"
74 < #include "openbabel/oopseformat.hpp"
75 < #include "openbabel/pdbformat.hpp"
76 < #include "openbabel/povrayformat.hpp"
77 < #include "openbabel/smilesformat.hpp"
78 < #include "openbabel/tinkerformat.hpp"
79 < #include "openbabel/xyzformat.hpp"
80 > namespace OpenMD {
81  
82  
82 – namespace oopse {
83 –
84 –
83    void registerForceFields() {
84      /** @todo move to a seperate initialization module */
85      //DUFF, WATER and LJ are merged into one force field
# Line 90 | Line 88 | namespace oopse {
88      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("LJ"));
89      //in theory, EAM can also be merged
90      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<EAM_FF>("EAM"));
91 +    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<EADM_FF>("EADM"));
92      //heck, that worked...  let's try merging SHAPES
93      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SHAPES_FF>("SHAPES"));
94      //Well if EAM worked... then Sutton-Chen should work like a CHARMM(Hopefully not).
95      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SC_FF>("SC"));
96 +    //Well if Sutton-Chen worked... then lets just mangle all of the forcefields together in MnM.
97 +    //That sounds like a good idea right......
98 +    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<MnM_FF>("MnM"));
99      ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<CLAYFF>("CLAY"));
100 +    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<Amber_FF>("Amber"));
101    }
102 <
102 >  
103    void registerIntegrators() {
104      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVE>("NVE"));
105      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVT>("NVT"));
# Line 106 | Line 109 | namespace oopse {
109      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPAT>("NPAT"));
110      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPRT"));
111      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPGT"));
112 +    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGT"));
113 +    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGAMMAT"));
114      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LANGEVINDYNAMICS"));
115      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LD"));
116 <    
117 <
116 > #if defined(HAVE_QHULL)
117 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LHULL"));
118 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LANGEVINHULL"));
119 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("SMIPD"));
120 > #endif
121    }
122  
123    void registerMinimizers() {
# Line 121 | Line 129 | namespace oopse {
129      LatticeFactory::getInstance()->registerLattice(new LatticeBuilder<FCCLattice>("FCC"));
130    }
131  
124 –  void registerOBFormats(){
125 –    static OpenBabel::AmberPrepFormat amberFormatInstance;
126 –    static OpenBabel::FingerprintFormat fingerprintFormatInstance;
127 –    static OpenBabel::OOPSEFormat oopseFormatInstance;    
128 –    static OpenBabel::PDBFormat pdbFormatInstance;
129 –    static OpenBabel::PovrayFormat povaryFormatInstance;
130 –    static OpenBabel::SMIFormat smilesFormatInstance;
131 –    static OpenBabel::TinkerFormat tinkerFormatInstance;
132 –    static OpenBabel::XYZFormat xyzFormatInstance;    
133 –  }
134 –  
132    void registerAll() {
133      registerForceFields();
134      registerIntegrators();

Comparing:
trunk/src/brains/Register.cpp (property svn:keywords), Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
branches/development/src/brains/Register.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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