src/brains/SimCreator.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.
 */
 
/**
 * @file SimCreatorr.hpp
 * @author tlin
 * @date 11/02/2004
 * @time 12:126am
 * @version 1.0
 */

#ifndef BRAINS_SIMCREATOR_HPP
#define BRAINS_SIMCREATOR_HPP


#include "primitives/Molecule.hpp"
#include "brains/SimInfo.hpp"
#include "types/MakeStamps.hpp"
#include "io/Globals.hpp"
#include "UseTheForce/ForceField.hpp"

// this routine is defined in BASS_interface.cpp
//another OOPS
extern void set_interface_stamps( MakeStamps* ms, Globals* g );

namespace oopse {

  /**
   * @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
   * The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo
   * instance based on the information returned by parser. 
   */
  class SimCreator {
  public:

    virtual ~SimCreator() {}

    /**
     * Setup Simulation
     * @return a pointer to SimInfo
     * @param mdfile the meta-data file name
     */
    SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true);
        
  private:
        
    /**
     * Parses the meta-data file
     * @param mdfile
     * @param stamps
     * @param simParams
     */
    void parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams);


    /** create the molecules belong to current processor*/
    virtual void createMolecules(SimInfo* info);

    /** 
     * Sets the global index for atoms, rigidbodies and cutoff groups and fill up
     * globalGroupMembership and globalMolMembership arrays which map atoms'
     * global index to the global index of the groups (or molecules) they belong to.
     * These array are never changed during the simulation.
     */
    void setGlobalIndex(SimInfo* info);

    void gatherParameters(SimInfo *info, const std::string& mdfile);             

        
    /** Extracts the molecules stamps and adds them into SimInfo class */
    void compList(MakeStamps* stamps,  Globals* simParams, 
                  std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ;

    /**
     * Divide the molecules among the processors 
     */
         
    void divideMolecules(SimInfo* info);

    /** Load initial coordinates */
    void loadCoordinates(SimInfo* info);     

    std::string mdFileName_;  //save the meta-data file name which may be used later
  };

} //end namespace oopse
#endif //BRAINS_SIMCREATOR_HPP

Revision:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	4399 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	Content
1	/*
2	* Copyright (c) 2005 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. 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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file SimCreatorr.hpp
44	* @author tlin
45	* @date 11/02/2004
46	* @time 12:126am
47	* @version 1.0
48	*/
49
50	#ifndef BRAINS_SIMCREATOR_HPP
51	#define BRAINS_SIMCREATOR_HPP
52
53
54	#include "primitives/Molecule.hpp"
55	#include "brains/SimInfo.hpp"
56	#include "types/MakeStamps.hpp"
57	#include "io/Globals.hpp"
58	#include "UseTheForce/ForceField.hpp"
59
60	// this routine is defined in BASS_interface.cpp
61	//another OOPS
62	extern void set_interface_stamps( MakeStamps* ms, Globals* g );
63
64	namespace oopse {
65
66	/**
67	* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
68	* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo
69	* instance based on the information returned by parser.
70	*/
71	class SimCreator {
72	public:
73
74	virtual ~SimCreator() {}
75
76	/**
77	* Setup Simulation
78	* @return a pointer to SimInfo
79	* @param mdfile the meta-data file name
80	*/
81	SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true);
82
83	private:
84
85	/**
86	* Parses the meta-data file
87	* @param mdfile
88	* @param stamps
89	* @param simParams
90	*/
91	void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams);
92
93
94	/** create the molecules belong to current processor*/
95	virtual void createMolecules(SimInfo* info);
96
97	/**
98	* Sets the global index for atoms, rigidbodies and cutoff groups and fill up
99	* globalGroupMembership and globalMolMembership arrays which map atoms'
100	* global index to the global index of the groups (or molecules) they belong to.
101	* These array are never changed during the simulation.
102	*/
103	void setGlobalIndex(SimInfo* info);
104
105	void gatherParameters(SimInfo *info, const std::string& mdfile);
106
107
108	/** Extracts the molecules stamps and adds them into SimInfo class */
109	void compList(MakeStamps* stamps, Globals* simParams,
110	std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ;
111
112	/**
113	* Divide the molecules among the processors
114	*/
115
116	void divideMolecules(SimInfo* info);
117
118	/** Load initial coordinates */
119	void loadCoordinates(SimInfo* info);
120
121	std::string mdFileName_; //save the meta-data file name which may be used later
122	};
123
124	} //end namespace oopse
125	#endif //BRAINS_SIMCREATOR_HPP
126