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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @file SimCreatorr.hpp
 * @author tlin
 * @date 11/02/2004
 * @time 12:126am
 * @version 1.0
 */

#ifndef BRAINS_SIMCREATOR_HPP
#define BRAINS_SIMCREATOR_HPP

#include <iostream>
#include "primitives/Molecule.hpp"
#include "brains/SimInfo.hpp"
#include "io/Globals.hpp"
#include "UseTheForce/ForceField.hpp"

namespace OpenMD {

  /**
   * @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(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine);


    /** 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, const std::string& mdFileName);     

    std::string mdFileName_;  //save the meta-data file name which may be used later
  };

} //end namespace OpenMD
#endif //BRAINS_SIMCREATOR_HPP

Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	4125 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42	gezelter	507	/**
43			* @file SimCreatorr.hpp
44			* @author tlin
45			* @date 11/02/2004
46			* @time 12:126am
47			* @version 1.0
48			*/
49	gezelter	246
50			#ifndef BRAINS_SIMCREATOR_HPP
51			#define BRAINS_SIMCREATOR_HPP
52
53	tim	1024	#include <iostream>
54	gezelter	246	#include "primitives/Molecule.hpp"
55			#include "brains/SimInfo.hpp"
56			#include "io/Globals.hpp"
57			#include "UseTheForce/ForceField.hpp"
58
59	gezelter	1390	namespace OpenMD {
60	gezelter	246
61	gezelter	507	/**
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	246
69	gezelter	507	virtual ~SimCreator() {}
70	tim	385
71	gezelter	507	/**
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	246
78	gezelter	507	private:
79	gezelter	246
80	gezelter	507	/**
81			* Parses the meta-data file
82			* @param mdfile
83	tim	770	* @return simParams
84	gezelter	507	*/
85	tim	1024	Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine);
86	gezelter	246
87
88	gezelter	507	/** create the molecules belong to current processor*/
89			virtual void createMolecules(SimInfo* info);
90	gezelter	246
91	gezelter	507	/**
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	246
99	gezelter	507	void gatherParameters(SimInfo *info, const std::string& mdfile);
100	gezelter	246
101	gezelter	507	/**
102			* Divide the molecules among the processors
103			*/
104	gezelter	246
105	gezelter	507	void divideMolecules(SimInfo* info);
106	gezelter	246
107	gezelter	507	/** Load initial coordinates */
108	tim	1024	void loadCoordinates(SimInfo* info, const std::string& mdFileName);
109	gezelter	246
110	gezelter	507	std::string mdFileName_; //save the meta-data file name which may be used later
111			};
112	gezelter	246
113	gezelter	1390	} //end namespace OpenMD
114	gezelter	246	#endif //BRAINS_SIMCREATOR_HPP
115