src/io/DumpReader.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).
 */
  
/** 
 * @file DumpReader.hpp 
 * @author tlin 
 * @date 11/15/2004 
 * @time 09:25am 
 * @version 2.0 
 */ 
 
#ifndef IO_DUMPREADER_HPP 
#define IO_DUMPREADER_HPP 
 
#include <cstdio> 
#include <string> 
#include "brains/SimInfo.hpp" 
#include "primitives/StuntDouble.hpp" 
namespace OpenMD { 
 
  /** 
   * @class DumpReader DumpReader.hpp "io/DumpReader.hpp" 
   * @todo get rid of more junk code from DumpReader 
   */ 
  class DumpReader { 
  public: 
 
    DumpReader(SimInfo* info, const std::string & filename); 
    //DumpReader(SimInfo * info, istream & is); 
 
    virtual ~DumpReader(); 
 
    /** Returns the number of frames in the dump file*/ 
    int getNFrames(); 
 
    void setNeedCOMprops(bool ncp) {
      needCOMprops_ = ncp;
    }
         
    virtual void readFrame(int whichFrame); 
 
  protected: 
 
    void scanFile();  
    void readSet(int whichFrame); 
    virtual void parseDumpLine(const std::string&); 
    virtual void parseSiteLine(const std::string&);  
    virtual void readFrameProperties(std::istream& inputStream);
    void readStuntDoubles(std::istream& inputStream);
    void readSiteData(std::istream& inputStream);
         
    SimInfo* info_; 
 
    std::string filename_; 
    bool isScanned_; 
 
    int nframes_; 
 
    std::istream* inFile_; 
     
    std::vector<std::streampos> framePos_; 
 
    bool needPos_; 
    bool needVel_; 
    bool needQuaternion_; 
    bool needAngMom_;
    bool needCOMprops_;

    const static int bufferSize = 4096;
    char buffer[bufferSize];
  }; 
 
}      //end namespace OpenMD 
 
#endif //IO_DUMPREADER_HPP 
Revision:	1752
Committed:	Sun Jun 10 14:05:02 2012 UTC (12 years, 10 months ago) by gezelter
File size:	3782 byte(s)
Log Message:	Added SiteData parsing and writing.
#	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, 24107 (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	/**
44	* @file DumpReader.hpp
45	* @author tlin
46	* @date 11/15/2004
47	* @time 09:25am
48	* @version 2.0
49	*/
50
51	#ifndef IO_DUMPREADER_HPP
52	#define IO_DUMPREADER_HPP
53
54	#include <cstdio>
55	#include <string>
56	#include "brains/SimInfo.hpp"
57	#include "primitives/StuntDouble.hpp"
58	namespace OpenMD {
59
60	/**
61	* @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
62	* @todo get rid of more junk code from DumpReader
63	*/
64	class DumpReader {
65	public:
66
67	DumpReader(SimInfo* info, const std::string & filename);
68	//DumpReader(SimInfo * info, istream & is);
69
70	virtual ~DumpReader();
71
72	/** Returns the number of frames in the dump file*/
73	int getNFrames();
74
75	void setNeedCOMprops(bool ncp) {
76	needCOMprops_ = ncp;
77	}
78
79	virtual void readFrame(int whichFrame);
80
81	protected:
82
83	void scanFile();
84	void readSet(int whichFrame);
85	virtual void parseDumpLine(const std::string&);
86	virtual void parseSiteLine(const std::string&);
87	virtual void readFrameProperties(std::istream& inputStream);
88	void readStuntDoubles(std::istream& inputStream);
89	void readSiteData(std::istream& inputStream);
90
91	SimInfo* info_;
92
93	std::string filename_;
94	bool isScanned_;
95
96	int nframes_;
97
98	std::istream* inFile_;
99
100	std::vector<std::streampos> framePos_;
101
102	bool needPos_;
103	bool needVel_;
104	bool needQuaternion_;
105	bool needAngMom_;
106	bool needCOMprops_;
107
108	const static int bufferSize = 4096;
109	char buffer[bufferSize];
110	};
111
112	} //end namespace OpenMD
113
114	#endif //IO_DUMPREADER_HPP