applications/hydrodynamics/BeadModel.hpp


/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
#ifndef APPLICATION_HYDRODYNAMICS_BEADMODEL_HPP
#define APPLICATION_HYDRODYNAMICS_BEADMODEL_HPP

#include "applications/hydrodynamics/ApproximationModel.hpp"
#include "openbabel/mol.hpp"

using namespace OpenBabel;
namespace oopse {

class BeadModel : public ApproximationModel {
    public:
        BeadModel(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info) {}
    private:
        virtual bool createBeads(std::vector<BeadParam>& beads);
        bool createSingleBead(Atom* atom, std::vector<BeadParam>& beads);        
};

}

#endif
Revision:	2734
Committed:	Tue Apr 25 13:35:42 2006 UTC (18 years, 2 months ago) by gezelter
File size:	2625 byte(s)
Log Message:	Using OpenBabel element table to pick vdw radii for hydrodynamics if the LJ sigma can't be found.
#	Content
1
2	/*
3	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
4	*
5	* The University of Notre Dame grants you ("Licensee") a
6	* non-exclusive, royalty free, license to use, modify and
7	* redistribute this software in source and binary code form, provided
8	* that the following conditions are met:
9	*
10	* 1. Acknowledgement of the program authors must be made in any
11	* publication of scientific results based in part on use of the
12	* program. An acceptable form of acknowledgement is citation of
13	* the article in which the program was described (Matthew
14	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
15	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
16	* Parallel Simulation Engine for Molecular Dynamics,"
17	* J. Comput. Chem. 26, pp. 252-271 (2005))
18	*
19	* 2. Redistributions of source code must retain the above copyright
20	* notice, this list of conditions and the following disclaimer.
21	*
22	* 3. Redistributions in binary form must reproduce the above copyright
23	* notice, this list of conditions and the following disclaimer in the
24	* documentation and/or other materials provided with the
25	* distribution.
26	*
27	* This software is provided "AS IS," without a warranty of any
28	* kind. All express or implied conditions, representations and
29	* warranties, including any implied warranty of merchantability,
30	* fitness for a particular purpose or non-infringement, are hereby
31	* excluded. The University of Notre Dame and its licensors shall not
32	* be liable for any damages suffered by licensee as a result of
33	* using, modifying or distributing the software or its
34	* derivatives. In no event will the University of Notre Dame or its
35	* licensors be liable for any lost revenue, profit or data, or for
36	* direct, indirect, special, consequential, incidental or punitive
37	* damages, however caused and regardless of the theory of liability,
38	* arising out of the use of or inability to use software, even if the
39	* University of Notre Dame has been advised of the possibility of
40	* such damages.
41	*/
42	#ifndef APPLICATION_HYDRODYNAMICS_BEADMODEL_HPP
43	#define APPLICATION_HYDRODYNAMICS_BEADMODEL_HPP
44
45	#include "applications/hydrodynamics/ApproximationModel.hpp"
46	#include "openbabel/mol.hpp"
47
48	using namespace OpenBabel;
49	namespace oopse {
50
51	class BeadModel : public ApproximationModel {
52	public:
53	BeadModel(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info) {}
54	private:
55	virtual bool createBeads(std::vector<BeadParam>& beads);
56	bool createSingleBead(Atom* atom, std::vector<BeadParam>& beads);
57	};
58
59	}
60
61	#endif