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root/OpenMD/branches/development/src/brains/Register.cpp

Comparing:
trunk/src/brains/Register.cpp (file contents), Revision 1024 by tim, Wed Aug 30 18:42:29 2006 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"
60	–	#include "UseTheForce/DUFF.hpp"
61	–	#include "UseTheForce/EAM_FF.hpp"
62	–	#include "UseTheForce/ForceFieldFactory.hpp"
63	–	#include "UseTheForce/ForceFieldCreator.hpp"
64	–	#include "UseTheForce/SHAPES_FF.hpp"
65	–	#include "UseTheForce/SC_FF.hpp"
66	–	#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"
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"
70	>	namespace OpenMD {
71
81	–
82	–	namespace oopse {
83	–
84	–
85	–	void registerForceFields() {
86	–	/** @todo move to a seperate initialization module */
87	–	//DUFF, WATER and LJ are merged into one force field
88	–	ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("DUFF"));
89	–	ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("WATER"));
90	–	ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("LJ"));
91	–	//in theory, EAM can also be merged
92	–	ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<EAM_FF>("EAM"));
93	–	//heck, that worked...  let's try merging SHAPES
94	–	ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SHAPES_FF>("SHAPES"));
95	–	//Well if EAM worked... then Sutton-Chen should work like a CHARMM(Hopefully not).
96	–	ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SC_FF>("SC"));
97	–	ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<CLAYFF>("CLAY"));
98	–	}
99	–
72		void registerIntegrators() {
73		IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVE>("NVE"));
74		IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVT>("NVT"));
#	Line 106 | Line 78 | namespace oopse {
78		IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPAT>("NPAT"));
79		IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPRT"));
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	<
86	<
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 121 | Line 98 | namespace oopse {
98		LatticeFactory::getInstance()->registerLattice(new LatticeBuilder<FCCLattice>("FCC"));
99		}
100
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	–
101		void registerAll() {
136	–	registerForceFields();
102		registerIntegrators();
103		registerMinimizers();
104		}

Comparing:
trunk/src/brains/Register.cpp (property svn:keywords), Revision 1024 by tim, Wed Aug 30 18:42:29 2006 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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