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:

        /**
         * 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:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	4528 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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	/**
75	* Setup Simulation
76	* @return a pointer to SimInfo
77	* @param mdfile the meta-data file name
78	*/
79	SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true);
80
81	private:
82
83	/**
84	* Parses the meta-data file
85	* @param mdfile
86	* @param stamps
87	* @param simParams
88	*/
89	void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams);
90
91
92	/** create the molecules belong to current processor*/
93	virtual void createMolecules(SimInfo* info);
94
95	/**
96	* Sets the global index for atoms, rigidbodies and cutoff groups and fill up
97	* globalGroupMembership and globalMolMembership arrays which map atoms'
98	* global index to the global index of the groups (or molecules) they belong to.
99	* These array are never changed during the simulation.
100	*/
101	void setGlobalIndex(SimInfo* info);
102
103	void gatherParameters(SimInfo *info, const std::string& mdfile);
104
105
106	/** Extracts the molecules stamps and adds them into SimInfo class */
107	void compList(MakeStamps* stamps, Globals* simParams,
108	std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ;
109
110	/**
111	* Divide the molecules among the processors
112	*/
113
114	void divideMolecules(SimInfo* info);
115
116	/** Load initial coordinates */
117	void loadCoordinates(SimInfo* info);
118
119	std::string mdFileName_; //save the meta-data file name which may be used later
120	};
121
122	} //end namespace oopse
123	#endif //BRAINS_SIMCREATOR_HPP
124