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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file SimCreator.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 "brains/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 mdFileVersion, int metaDataStartingLine);


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

    /**
     * Figure out the data storage layout based on what kinds of
     * objects are being simulated
     */
    int computeStorageLayout(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:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
File size:	4388 byte(s)
Log Message:	Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44	gezelter	1710	* @file SimCreator.hpp
45	gezelter	507	* @author tlin
46			* @date 11/02/2004
47			* @time 12:126am
48			* @version 1.0
49			*/
50	gezelter	246
51			#ifndef BRAINS_SIMCREATOR_HPP
52			#define BRAINS_SIMCREATOR_HPP
53
54	tim	1024	#include <iostream>
55	gezelter	246	#include "primitives/Molecule.hpp"
56			#include "brains/SimInfo.hpp"
57			#include "io/Globals.hpp"
58	gezelter	1725	#include "brains/ForceField.hpp"
59	gezelter	246
60	gezelter	1390	namespace OpenMD {
61	gezelter	246
62	gezelter	507	/**
63			* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
64	gezelter	1549	*
65			* The only responsibility of SimCreator is to parse the meta-data
66			* file and create a SimInfo instance based on the information
67			* returned by parser.
68	gezelter	507	*/
69			class SimCreator {
70			public:
71	gezelter	246
72	gezelter	507	virtual ~SimCreator() {}
73	tim	385
74	gezelter	507	/**
75			* Setup Simulation
76			* @return a pointer to SimInfo
77			* @param mdfile the meta-data file name
78			*/
79			SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true);
80	gezelter	246
81	gezelter	507	private:
82	gezelter	246
83	gezelter	507	/**
84			* Parses the meta-data file
85			* @param mdfile
86	tim	770	* @return simParams
87	gezelter	507	*/
88	gezelter	1613	Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine);
89	gezelter	246
90
91	gezelter	507	/** create the molecules belong to current processor*/
92			virtual void createMolecules(SimInfo* info);
93	gezelter	1710
94			/**
95			* Figure out the data storage layout based on what kinds of
96			* objects are being simulated
97			*/
98			int computeStorageLayout(SimInfo* info);
99	gezelter	1549
100	gezelter	507	/**
101	gezelter	1549	* Sets the global index for atoms, rigidbodies and cutoff groups
102			* and fill up globalGroupMembership and globalMolMembership
103			* arrays which map atoms' global index to the global index of the
104			* groups (or molecules) they belong to. These array are never
105			* changed during the simulation.
106	gezelter	507	*/
107			void setGlobalIndex(SimInfo* info);
108	gezelter	246
109	gezelter	507	void gatherParameters(SimInfo *info, const std::string& mdfile);
110	gezelter	246
111	gezelter	507	/**
112			* Divide the molecules among the processors
113			*/
114	gezelter	246
115	gezelter	507	void divideMolecules(SimInfo* info);
116	gezelter	246
117	gezelter	507	/** Load initial coordinates */
118	tim	1024	void loadCoordinates(SimInfo* info, const std::string& mdFileName);
119	gezelter	246
120	gezelter	507	std::string mdFileName_; //save the meta-data file name which may be used later
121	gezelter	1549
122	gezelter	507	};
123	gezelter	246
124	gezelter	1390	} //end namespace OpenMD
125	gezelter	246	#endif //BRAINS_SIMCREATOR_HPP
126