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, 234107 (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 needSitePotential_;
    bool doSiteData_;
    bool createDumpFile_;
  };

}
#endif //#define IO_DUMPWRITER_HPP
Revision:	1993
Committed:	Tue Apr 29 17:32:31 2014 UTC (11 years ago) by gezelter
File size:	3758 byte(s)
Log Message:	Added sitePotentials for the Choi et al. potential-frequency maps for nitriles
#	Content
1	/*
2	* Copyright (c) 2009 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	// #include <unistd.h>
57	#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	namespace OpenMD {
66
67	/**
68	* @class DumpWriter DumpWriter.hpp "io/DumpWriter.hpp"
69	* @todo
70	*/
71	class DumpWriter{
72
73	public:
74	DumpWriter(SimInfo* info);
75	DumpWriter(SimInfo* info, const std::string& filename);
76	DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile);
77	~DumpWriter();
78
79	void writeDumpAndEor();
80	void writeDump();
81	void writeEor();
82
83	private:
84
85	void writeFrame(std::ostream& os);
86	void writeFrameProperties(std::ostream& os, Snapshot* s);
87	std::string prepareDumpLine(StuntDouble* sd);
88	std::string prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex);
89	std::ostream* createOStream(const std::string& filename);
90	void writeClosing(std::ostream& os);
91
92	SimInfo* info_;
93	std::string filename_;
94	std::ostream* dumpFile_;
95	std::string eorFilename_;
96	bool needCompression_;
97	bool needForceVector_;
98	bool needParticlePot_;
99	bool needFlucQ_;
100	bool needElectricField_;
101	bool needSitePotential_;
102	bool doSiteData_;
103	bool createDumpFile_;
104	};
105
106	}
107	#endif //#define IO_DUMPWRITER_HPP