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 "io/Globals.hpp"
#include "UseTheForce/ForceField.hpp"

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
     * @return simParams
     */
    Globals*  parseFile(const std::string mdFileName);


    /** 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);             
        
    /**
     * 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:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (18 years, 8 months ago) by tim
File size:	3978 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
43			* @file SimCreatorr.hpp
44			* @author tlin
45			* @date 11/02/2004
46			* @time 12:126am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#ifndef BRAINS_SIMCREATOR_HPP
51			#define BRAINS_SIMCREATOR_HPP
52
53
54			#include "primitives/Molecule.hpp"
55			#include "brains/SimInfo.hpp"
56			#include "io/Globals.hpp"
57			#include "UseTheForce/ForceField.hpp"
58
59			namespace oopse {
60
61	gezelter	2204	/**
62			* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
63			* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo
64			* instance based on the information returned by parser.
65			*/
66			class SimCreator {
67			public:
68	gezelter	1930
69	gezelter	2204	virtual ~SimCreator() {}
70	tim	2069
71	gezelter	2204	/**
72			* Setup Simulation
73			* @return a pointer to SimInfo
74			* @param mdfile the meta-data file name
75			*/
76			SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true);
77	gezelter	1930
78	gezelter	2204	private:
79	gezelter	1930
80	gezelter	2204	/**
81			* Parses the meta-data file
82			* @param mdfile
83	tim	2469	* @return simParams
84	gezelter	2204	*/
85	tim	2469	Globals* parseFile(const std::string mdFileName);
86	gezelter	1930
87
88	gezelter	2204	/** create the molecules belong to current processor*/
89			virtual void createMolecules(SimInfo* info);
90	gezelter	1930
91	gezelter	2204	/**
92			* Sets the global index for atoms, rigidbodies and cutoff groups and fill up
93			* globalGroupMembership and globalMolMembership arrays which map atoms'
94			* global index to the global index of the groups (or molecules) they belong to.
95			* These array are never changed during the simulation.
96			*/
97			void setGlobalIndex(SimInfo* info);
98	gezelter	1930
99	gezelter	2204	void gatherParameters(SimInfo *info, const std::string& mdfile);
100	gezelter	1930
101	gezelter	2204	/**
102			* Divide the molecules among the processors
103			*/
104	gezelter	1930
105	gezelter	2204	void divideMolecules(SimInfo* info);
106	gezelter	1930
107	gezelter	2204	/** Load initial coordinates */
108			void loadCoordinates(SimInfo* info);
109	gezelter	1930
110	gezelter	2204	std::string mdFileName_; //save the meta-data file name which may be used later
111			};
112	gezelter	1930
113			} //end namespace oopse
114			#endif //BRAINS_SIMCREATOR_HPP
115