src/brains/SimCreator.hpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
 /**
  * @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);
        
    private:
        
        /**
         * Parses the meta-data file
         * @param mdfile
         * @param stamps
         * @param globals
         */
        void parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* globals);


        /** 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* globals, 
                                     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:	1807
Committed:	Tue Nov 30 22:43:51 2004 UTC (19 years, 9 months ago) by tim
File size:	3564 byte(s)
Log Message:	brains get built
#	User	Rev	Content
1	tim	1703	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25
26			/**
27			* @file SimCreatorr.hpp
28			* @author tlin
29			* @date 11/02/2004
30			* @time 12:126am
31			* @version 1.0
32			*/
33
34			#ifndef BRAINS_SIMCREATOR_HPP
35			#define BRAINS_SIMCREATOR_HPP
36
37
38	tim	1712	#include "primitives/Molecule.hpp"
39	tim	1804	#include "brains/SimInfo.hpp"
40	tim	1712	#include "types/MakeStamps.hpp"
41			#include "io/Globals.hpp"
42			#include "UseTheForce/ForceField.hpp"
43
44	tim	1807	// this routine is defined in BASS_interface.cpp
45			//another OOPS
46			extern void set_interface_stamps( MakeStamps* ms, Globals* g );
47
48	tim	1703	namespace oopse {
49
50			/**
51			* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
52	tim	1738	* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo
53			* instance based on the information returned by parser.
54	tim	1703	*/
55			class SimCreator {
56			public:
57	tim	1712
58	tim	1733	/**
59			* Setup Simulation
60			* @return a pointer to SimInfo
61			* @param mdfile the meta-data file name
62			*/
63	tim	1775	SimInfo* createSim(const std::string & mdFileName);
64	tim	1703
65	tim	1807	private:
66
67	tim	1733	/**
68			* Parses the meta-data file
69			* @param mdfile
70			* @param stamps
71			* @param globals
72			*/
73			void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* globals);
74
75	tim	1725
76	tim	1733	/** create the molecules belong to current processor*/
77	tim	1807	virtual void createMolecules(SimInfo* info);
78	tim	1733
79	tim	1735	/**
80			* Sets the global index for atoms, rigidbodies and cutoff groups and fill up
81			* globalGroupMembership and globalMolMembership arrays which map atoms'
82			* global index to the global index of the groups (or molecules) they belong to.
83			* These array are never changed during the simulation.
84			*/
85	tim	1807	void setGlobalIndex(SimInfo* info);
86
87			void gatherParameters(SimInfo *info, const std::string& mdfile);
88
89	tim	1733
90			/** Extracts the molecules stamps and adds them into SimInfo class */
91			void compList(MakeStamps* stamps, Globals* globals,
92			std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ;
93	tim	1807
94			/**
95			* Divide the molecules among the processors
96			*/
97
98			void divideMolecules(SimInfo* info);
99
100			/** Load initial coordinates */
101			void loadCoordinates(SimInfo* info);
102
103	tim	1733	std::string mdFileName_; //save the meta-data file name which may be used later
104	tim	1703	};
105
106			} //end namespace oopse
107			#endif //BRAINS_SIMCREATOR_HPP