src/io/DumpWriter.hpp

/*
 * Copyright (c) 2009 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).
 */
 
#ifndef IO_DUMPWRITER_HPP
#define IO_DUMPWRITER_HPP

#define _LARGEFILE_SOURCE64
#ifndef _FILE_OFFSET_BITS
#define _FILE_OFFSET_BITS 64
#endif
#include <iostream>
#include <fstream>
#include <string>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
// #include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>

#include "primitives/Atom.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "primitives/StuntDouble.hpp"

namespace OpenMD {

  /**
   * @class DumpWriter DumpWriter.hpp "io/DumpWriter.hpp"
   * @todo 
   */
  class DumpWriter{

  public:
    DumpWriter(SimInfo* info);
    DumpWriter(SimInfo* info, const std::string& filename);
    DumpWriter(SimInfo* info, const std::string& filename,  bool writeDumpFile);
    ~DumpWriter();

    void writeDumpAndEor();
    void writeDump();
    void writeEor();
    
  private:  
        
    void writeFrame(std::ostream& os);
    void writeFrameProperties(std::ostream& os, Snapshot* s);
    std::string prepareDumpLine(StuntDouble* sd);
    std::string prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex);
    std::ostream* createOStream(const std::string& filename);
    void writeClosing(std::ostream& os);
    
    SimInfo* info_;
    std::string filename_;
    std::ostream* dumpFile_;
    std::string eorFilename_;
    bool needCompression_;
    bool needForceVector_;
    bool needParticlePot_;
    bool needFlucQ_;
    bool needElectricField_;
    bool doSiteData_;
    bool createDumpFile_;
  };

}
#endif //#define IO_DUMPWRITER_HPP
Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (13 years, 2 months ago) by gezelter
File size:	3728 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	1390	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	gezelter	246	*
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	1782	* [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			#ifndef IO_DUMPWRITER_HPP
44			#define IO_DUMPWRITER_HPP
45
46			#define _LARGEFILE_SOURCE64
47			#ifndef _FILE_OFFSET_BITS
48			#define _FILE_OFFSET_BITS 64
49			#endif
50			#include <iostream>
51			#include <fstream>
52			#include <string>
53			#include <string.h>
54			#include <stdio.h>
55			#include <stdlib.h>
56	gezelter	1782	// #include <unistd.h>
57	gezelter	246	#include <sys/types.h>
58			#include <sys/stat.h>
59
60			#include "primitives/Atom.hpp"
61			#include "brains/SimInfo.hpp"
62			#include "brains/Thermo.hpp"
63			#include "primitives/StuntDouble.hpp"
64
65	gezelter	1390	namespace OpenMD {
66	gezelter	246
67	gezelter	507	/**
68			* @class DumpWriter DumpWriter.hpp "io/DumpWriter.hpp"
69			* @todo
70			*/
71			class DumpWriter{
72	gezelter	246
73	gezelter	507	public:
74			DumpWriter(SimInfo* info);
75			DumpWriter(SimInfo* info, const std::string& filename);
76	chuckv	791	DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile);
77	gezelter	507	~DumpWriter();
78	tim	376
79	gezelter	507	void writeDumpAndEor();
80			void writeDump();
81			void writeEor();
82	chuckv	791
83	gezelter	507	private:
84	tim	376
85	gezelter	507	void writeFrame(std::ostream& os);
86	tim	1024	void writeFrameProperties(std::ostream& os, Snapshot* s);
87	gezelter	1782	std::string prepareDumpLine(StuntDouble* sd);
88			std::string prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex);
89	tim	615	std::ostream* createOStream(const std::string& filename);
90	tim	1024	void writeClosing(std::ostream& os);
91	tim	615
92	gezelter	507	SimInfo* info_;
93			std::string filename_;
94	tim	615	std::ostream* dumpFile_;
95	gezelter	507	std::string eorFilename_;
96	tim	615	bool needCompression_;
97	chrisfen	721	bool needForceVector_;
98	gezelter	1610	bool needParticlePot_;
99	gezelter	1782	bool needFlucQ_;
100			bool needElectricField_;
101			bool doSiteData_;
102	chuckv	791	bool createDumpFile_;
103	gezelter	507	};
104	gezelter	246
105			}
106			#endif //#define IO_DUMPWRITER_HPP