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, 234107 (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 
 * @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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	3765 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	gezelter	1390	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	1390	*/
42	chrisfen	721
43			/**
44			* @file DumpReader.hpp
45			* @author tlin
46			* @date 11/15/2004
47			* @version 2.0
48			*/
49
50			#ifndef IO_DUMPREADER_HPP
51			#define IO_DUMPREADER_HPP
52
53			#include <cstdio>
54			#include <string>
55			#include "brains/SimInfo.hpp"
56			#include "primitives/StuntDouble.hpp"
57	gezelter	1390	namespace OpenMD {
58	chrisfen	721
59			/**
60			* @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
61			* @todo get rid of more junk code from DumpReader
62			*/
63			class DumpReader {
64			public:
65
66			DumpReader(SimInfo* info, const std::string & filename);
67			//DumpReader(SimInfo * info, istream & is);
68
69	cli2	1360	virtual ~DumpReader();
70	chrisfen	721
71			/** Returns the number of frames in the dump file*/
72			int getNFrames();
73
74	gezelter	1104	void setNeedCOMprops(bool ncp) {
75			needCOMprops_ = ncp;
76			}
77	chrisfen	721
78	cli2	1360	virtual void readFrame(int whichFrame);
79	chrisfen	721
80	cli2	1360	protected:
81	chrisfen	721
82	gezelter	1782	void scanFile();
83	chrisfen	721	void readSet(int whichFrame);
84	cli2	1360	virtual void parseDumpLine(const std::string&);
85	gezelter	1782	virtual void parseSiteLine(const std::string&);
86	cli2	1360	virtual void readFrameProperties(std::istream& inputStream);
87	gezelter	1782	void readStuntDoubles(std::istream& inputStream);
88			void readSiteData(std::istream& inputStream);
89	chrisfen	721
90			SimInfo* info_;
91
92			std::string filename_;
93			bool isScanned_;
94
95			int nframes_;
96
97			std::istream* inFile_;
98
99			std::vector<std::streampos> framePos_;
100
101			bool needPos_;
102			bool needVel_;
103			bool needQuaternion_;
104	gezelter	1104	bool needAngMom_;
105			bool needCOMprops_;
106	tim	1024
107			const static int bufferSize = 4096;
108			char buffer[bufferSize];
109	chrisfen	721	};
110
111	gezelter	1390	} //end namespace OpenMD
112	chrisfen	721
113			#endif //IO_DUMPREADER_HPP