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Comparing:
trunk/src/brains/Register.cpp (file contents), Revision 788 by gezelter, Mon Dec 5 22:23:57 2005 UTC vs.
branches/development/src/brains/Register.cpp (file contents), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 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"
64   #include "minimizers/PRCG.hpp"
65   #include "minimizers/SDMinimizer.hpp"
59 – #include "UseTheForce/DUFF.hpp"
60 – #include "UseTheForce/EAM_FF.hpp"
61 – #include "UseTheForce/ForceFieldFactory.hpp"
62 – #include "UseTheForce/ForceFieldCreator.hpp"
63 – #include "UseTheForce/SHAPES_FF.hpp"
64 – #include "UseTheForce/SC_FF.hpp"
65 – #include "UseTheForce/CLAYFF.hpp"
66   #include "lattice/LatticeFactory.hpp"
67   #include "lattice/LatticeCreator.hpp"
68   #include "lattice/FCCLattice.hpp"
69  
70 < #include "openbabel/amberformat.hpp"
71 < #include "openbabel/fingerprintformat.hpp"
72 < #include "openbabel/gromos96format.hpp"
73 < #include "openbabel/oopseformat.hpp"
74 < #include "openbabel/pdbformat.hpp"
75 < #include "openbabel/povrayformat.hpp"
76 < #include "openbabel/smilesformat.hpp"
77 < #include "openbabel/tinkerformat.hpp"
78 < #include "openbabel/xyzformat.hpp"
70 > namespace OpenMD {
71  
80 –
81 – namespace oopse {
82 –
83 –
84 –  void registerForceFields() {
85 –    /** @todo move to a seperate initialization module */
86 –    //DUFF, WATER and LJ are merged into one force field
87 –    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("DUFF"));
88 –    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("WATER"));
89 –    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("LJ"));
90 –    //in theory, EAM can also be merged
91 –    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<EAM_FF>("EAM"));
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 –    ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<CLAYFF>("CLAY"));
97 –  }
98 –
72    void registerIntegrators() {
73      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVE>("NVE"));
74      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVT>("NVT"));
# Line 104 | Line 77 | namespace oopse {
77      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPTxyz>("NPTXYZ"));
78      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPAT>("NPAT"));
79      IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPRT"));
80 <
80 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPGT"));
81 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGT"));
82 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGAMMAT"));
83 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LANGEVINDYNAMICS"));
84 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LD"));
85 > #if defined(HAVE_QHULL)
86 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LHULL"));
87 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LANGEVINHULL"));
88 >    IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("SMIPD"));
89 > #endif
90    }
91  
92    void registerMinimizers() {
# Line 116 | Line 98 | namespace oopse {
98      LatticeFactory::getInstance()->registerLattice(new LatticeBuilder<FCCLattice>("FCC"));
99    }
100  
119 –  void registerOBFormats(){
120 –    static OpenBabel::AmberPrepFormat amberFormatInstance;
121 –    static OpenBabel::FingerprintFormat fingerprintFormatInstance;
122 –    static OpenBabel::OOPSEFormat oopseFormatInstance;    
123 –    static OpenBabel::PDBFormat pdbFormatInstance;
124 –    static OpenBabel::PovrayFormat povaryFormatInstance;
125 –    static OpenBabel::SMIFormat smilesFormatInstance;
126 –    static OpenBabel::TinkerFormat tinkerFormatInstance;
127 –    static OpenBabel::XYZFormat xyzFormatInstance;    
128 –  }
129 –  
101    void registerAll() {
131 –    registerForceFields();
102      registerIntegrators();
103      registerMinimizers();
104    }

Comparing:
trunk/src/brains/Register.cpp (property svn:keywords), Revision 788 by gezelter, Mon Dec 5 22:23:57 2005 UTC vs.
branches/development/src/brains/Register.cpp (property svn:keywords), Revision 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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