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.
#	User	Rev	Content
1	tim	2623
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	tim	2634	#include "applications/hydrodynamics/ApproximationModel.hpp"
46	gezelter	2734	#include "openbabel/mol.hpp"
47	tim	2623
48	gezelter	2734	using namespace OpenBabel;
49	tim	2623	namespace oopse {
50
51	tim	2634	class BeadModel : public ApproximationModel {
52	tim	2623	public:
53	tim	2634	BeadModel(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info) {}
54	tim	2623	private:
55			virtual bool createBeads(std::vector<BeadParam>& beads);
56			bool createSingleBead(Atom* atom, std::vector<BeadParam>& beads);
57			};
58
59			}
60
61			#endif