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, 3 months ago) by gezelter
File size:	4399 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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 "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	gezelter	2204	/**
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	gezelter	1930
74	gezelter	2204	virtual ~SimCreator() {}
75	tim	2069
76	gezelter	2204	/**
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	gezelter	1930
83	gezelter	2204	private:
84	gezelter	1930
85	gezelter	2204	/**
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	gezelter	1930
93
94	gezelter	2204	/** create the molecules belong to current processor*/
95			virtual void createMolecules(SimInfo* info);
96	gezelter	1930
97	gezelter	2204	/**
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	gezelter	1930
105	gezelter	2204	void gatherParameters(SimInfo *info, const std::string& mdfile);
106	gezelter	1930
107
108	gezelter	2204	/** 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	gezelter	1930
112	gezelter	2204	/**
113			* Divide the molecules among the processors
114			*/
115	gezelter	1930
116	gezelter	2204	void divideMolecules(SimInfo* info);
117	gezelter	1930
118	gezelter	2204	/** Load initial coordinates */
119			void loadCoordinates(SimInfo* info);
120	gezelter	1930
121	gezelter	2204	std::string mdFileName_; //save the meta-data file name which may be used later
122			};
123	gezelter	1930
124			} //end namespace oopse
125			#endif //BRAINS_SIMCREATOR_HPP
126