src/integrators/SMIPDForceManager.hpp

/*
 * Copyright (c) 2008, 2010 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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#ifndef INTEGRATOR_SMIPDFORCEMANAGER_HPP
#define INTEGRATOR_SMIPDFORCEMANAGER_HPP

#include "brains/ForceManager.hpp"
#include "brains/Thermo.hpp"
#include "primitives/Molecule.hpp"
#include "integrators/Velocitizer.hpp"
#include "math/Hull.hpp"
#include "math/Triangle.hpp"
#include "math/SeqRandNumGen.hpp"

namespace OpenMD {
   
  /**
   * @class SMIDForceManager
   * Force manager for Surface Mesh Implicit Pressure Dynamics
   * applying friction and random forces as well as torques. 
   * Stochasitc force is determined by area of surface triangles 
   * on the convex hull. See: Kohanoff et al. CHEMPHYSCHEM 2005, 6, 1848-1852.
   */
  class SMIPDForceManager : public ForceManager{
    
  public:
    SMIPDForceManager(SimInfo * info);
    
  protected:
    virtual void postCalculation(bool needStress);
    
  private:
    std::vector<Vector3d> genTriangleForces(int nTriangles, RealType variance);

    Globals* simParams;
    SeqRandNumGen randNumGen_;    
    Velocitizer* veloMunge;

    RealType dt_;
    RealType targetTemp_;
    RealType targetPressure_; 
    RealType viscosity_;

    RealType variance_;

  enum HullTypeEnum {
      hullConvex,
      hullAlphaShape,
      hullUnknown
    };
    
    std::map<std::string, HullTypeEnum> stringToEnumMap_;
    HullTypeEnum hullType_;


    Hull* surfaceMesh_;
    std::vector<StuntDouble*> localSites_;
  };
  
} //end namespace OpenMD
#endif //SIMPD_FORCEMANAGER

Revision:	1402
Committed:	Fri Jan 8 17:15:27 2010 UTC (15 years, 4 months ago) by chuckv
File size:	3564 byte(s)
Log Message:	Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
#	Content
1	/*
2	* Copyright (c) 2008, 2010 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#ifndef INTEGRATOR_SMIPDFORCEMANAGER_HPP
43	#define INTEGRATOR_SMIPDFORCEMANAGER_HPP
44
45	#include "brains/ForceManager.hpp"
46	#include "brains/Thermo.hpp"
47	#include "primitives/Molecule.hpp"
48	#include "integrators/Velocitizer.hpp"
49	#include "math/Hull.hpp"
50	#include "math/Triangle.hpp"
51	#include "math/SeqRandNumGen.hpp"
52
53	namespace OpenMD {
54
55	/**
56	* @class SMIDForceManager
57	* Force manager for Surface Mesh Implicit Pressure Dynamics
58	* applying friction and random forces as well as torques.
59	* Stochasitc force is determined by area of surface triangles
60	* on the convex hull. See: Kohanoff et al. CHEMPHYSCHEM 2005, 6, 1848-1852.
61	*/
62	class SMIPDForceManager : public ForceManager{
63
64	public:
65	SMIPDForceManager(SimInfo * info);
66
67	protected:
68	virtual void postCalculation(bool needStress);
69
70	private:
71	std::vector<Vector3d> genTriangleForces(int nTriangles, RealType variance);
72
73	Globals* simParams;
74	SeqRandNumGen randNumGen_;
75	Velocitizer* veloMunge;
76
77	RealType dt_;
78	RealType targetTemp_;
79	RealType targetPressure_;
80	RealType viscosity_;
81
82	RealType variance_;
83
84	enum HullTypeEnum {
85	hullConvex,
86	hullAlphaShape,
87	hullUnknown
88	};
89
90	std::map<std::string, HullTypeEnum> stringToEnumMap_;
91	HullTypeEnum hullType_;
92
93
94
95	Hull* surfaceMesh_;
96	std::vector<StuntDouble*> localSites_;
97	};
98
99	} //end namespace OpenMD
100	#endif //SIMPD_FORCEMANAGER
101