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 "brans/SimInfo.hpp"
#include "types/MakeStamps.hpp"
#include "io/Globals.hpp"
#include "UseTheForce/ForceField.hpp"

namespace oopse {

/**
 * @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
 * @brief 
 */
class SimCreator {
    public:

        /**
         * Setup Simulation
         * @return a pointer to SimInfo
         * @param mdfile the meta-data file name
         */
        SimInfo* createSim(char* mdfile);
        
    protected:

        /**
         * Parses the meta-data file
         * @param mdfile
         * @param stamps
         * @param globals
         */
        void parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* globals);

#ifdef IS_MPI
        /**
         * Divide the molecules among the processors 
         */
        void divideMolecules();
#endif //is_mpi

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

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

        /** Initialize fortran, mainly set the cutoff radius and setup*/
        void initFortran(SimInfo* info);

        /** Figure out the cutoff radius and pass it to fortran */
        void setCutoff(SimInfo* info);
        
        std::string mdFileName_;  //save the meta-data file name which may be used later
};

} //end namespace oopse
#endif //BRAINS_SIMCREATOR_HPP
Revision:	1735
Committed:	Fri Nov 12 17:40:03 2004 UTC (19 years, 9 months ago) by tim
File size:	3327 byte(s)
Log Message:	SimCreator and SimInfo are ready for unit test
#	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			#include "brans/SimInfo.hpp"
40			#include "types/MakeStamps.hpp"
41			#include "io/Globals.hpp"
42			#include "UseTheForce/ForceField.hpp"
43
44	tim	1703	namespace oopse {
45
46			/**
47			* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
48	tim	1733	* @brief
49	tim	1703	*/
50			class SimCreator {
51			public:
52	tim	1712
53	tim	1733	/**
54			* Setup Simulation
55			* @return a pointer to SimInfo
56			* @param mdfile the meta-data file name
57			*/
58	tim	1712	SimInfo* createSim(char* mdfile);
59	tim	1703
60			protected:
61	tim	1713
62	tim	1733	/**
63			* Parses the meta-data file
64			* @param mdfile
65			* @param stamps
66			* @param globals
67			*/
68			void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* globals);
69
70	tim	1713	#ifdef IS_MPI
71	tim	1733	/**
72			* Divide the molecules among the processors
73			*/
74	tim	1727	void divideMolecules();
75	tim	1713	#endif //is_mpi
76	tim	1725
77	tim	1733	/** create the molecules belong to current processor*/
78			virtual void createMolecules();
79
80	tim	1735	/**
81			* Sets the global index for atoms, rigidbodies and cutoff groups and fill up
82			* globalGroupMembership and globalMolMembership arrays which map atoms'
83			* global index to the global index of the groups (or molecules) they belong to.
84			* These array are never changed during the simulation.
85			*/
86	tim	1733	void setGlobalIndex();
87	tim	1713
88	tim	1719	private:
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
94			/** Initialize fortran, mainly set the cutoff radius and setup*/
95			void initFortran(SimInfo* info);
96
97	tim	1735	/** Figure out the cutoff radius and pass it to fortran */
98			void setCutoff(SimInfo* info);
99
100	tim	1733	std::string mdFileName_; //save the meta-data file name which may be used later
101	tim	1703	};
102
103			} //end namespace oopse
104			#endif //BRAINS_SIMCREATOR_HPP