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
 * @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 mdFileName the meta-data file name
     * @param loadInitCoords should the initial coordinates be loaded from a file?
     */
    SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true);
        
  private:
        
    /**
     * Parses the meta-data file
     * @param mdFileName the meta-data file name
     * @param rawMetaData the raw meta-data stream
     * @param mdFileVersion the version of code used to create the meta-data file
     * @param metaDataStartingLine the starting line of the meta-data block
     * @return a pointer to the simulation parameters in a #Globals object
     */
    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:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	4744 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	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			* @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	gezelter	1725	#include "brains/ForceField.hpp"
58	gezelter	246
59	gezelter	1390	namespace OpenMD {
60	gezelter	246
61	gezelter	507	/**
62			* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
63	gezelter	1549	*
64			* The only responsibility of SimCreator is to parse the meta-data
65			* file and create a SimInfo instance based on the information
66			* returned by parser.
67	gezelter	507	*/
68			class SimCreator {
69			public:
70	gezelter	246
71	gezelter	507	virtual ~SimCreator() {}
72	tim	385
73	gezelter	507	/**
74			* Setup Simulation
75			* @return a pointer to SimInfo
76	gezelter	1808	* @param mdFileName the meta-data file name
77			* @param loadInitCoords should the initial coordinates be loaded from a file?
78	gezelter	507	*/
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	gezelter	1808	* @param mdFileName the meta-data file name
86			* @param rawMetaData the raw meta-data stream
87			* @param mdFileVersion the version of code used to create the meta-data file
88			* @param metaDataStartingLine the starting line of the meta-data block
89			* @return a pointer to the simulation parameters in a #Globals object
90	gezelter	507	*/
91	gezelter	1613	Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine);
92	gezelter	246
93
94	gezelter	507	/** create the molecules belong to current processor*/
95			virtual void createMolecules(SimInfo* info);
96	gezelter	1710
97			/**
98			* Figure out the data storage layout based on what kinds of
99			* objects are being simulated
100			*/
101			int computeStorageLayout(SimInfo* info);
102	gezelter	1549
103	gezelter	507	/**
104	gezelter	1549	* Sets the global index for atoms, rigidbodies and cutoff groups
105			* and fill up globalGroupMembership and globalMolMembership
106			* arrays which map atoms' global index to the global index of the
107			* groups (or molecules) they belong to. These array are never
108			* changed during the simulation.
109	gezelter	507	*/
110			void setGlobalIndex(SimInfo* info);
111	gezelter	246
112	gezelter	507	void gatherParameters(SimInfo *info, const std::string& mdfile);
113	gezelter	246
114	gezelter	507	/**
115			* Divide the molecules among the processors
116			*/
117	gezelter	246
118	gezelter	507	void divideMolecules(SimInfo* info);
119	gezelter	246
120	gezelter	507	/** Load initial coordinates */
121	tim	1024	void loadCoordinates(SimInfo* info, const std::string& mdFileName);
122	gezelter	246
123	gezelter	507	std::string mdFileName_; //save the meta-data file name which may be used later
124	gezelter	1549
125	gezelter	507	};
126	gezelter	246
127	gezelter	1390	} //end namespace OpenMD
128	gezelter	246	#endif //BRAINS_SIMCREATOR_HPP
129