src/io/DumpReader.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. Acknowledgement of the program authors must be made in any 
 *    publication of scientific results based in part on use of the 
 *    program.  An acceptable form of acknowledgement is citation of 
 *    the article in which the program was described (Matthew 
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher 
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented 
 *    Parallel Simulation Engine for Molecular Dynamics," 
 *    J. Comput. Chem. 26, pp. 252-271 (2005)) 
 * 
 * 2. Redistributions of source code must retain the above copyright 
 *    notice, this list of conditions and the following disclaimer. 
 * 
 * 3. 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. 
 */ 
  
/** 
 * @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 oopse { 
 
  /** 
   * @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 readFrameProperties(std::istream& inputStream);

    void readStuntDoubles(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 oopse 
 
#endif //IO_DUMPREADER_HPP 
Revision:	1360
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 7 months ago) by cli2
Original Path:	*trunk/src/io/DumpReader.hpp*
File size:	3633 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	User	Rev	Content
1	chrisfen	721	/*
2			* 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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file DumpReader.hpp
44			* @author tlin
45			* @date 11/15/2004
46			* @time 09:25am
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			namespace oopse {
58
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			void scanFile();
83
84			void readSet(int whichFrame);
85
86	cli2	1360	virtual void parseDumpLine(const std::string&);
87	chrisfen	721
88	cli2	1360	virtual void readFrameProperties(std::istream& inputStream);
89	tim	1024
90	gezelter	1104	void readStuntDoubles(std::istream& inputStream);
91	chrisfen	721
92			SimInfo* info_;
93
94			std::string filename_;
95			bool isScanned_;
96
97			int nframes_;
98
99			std::istream* inFile_;
100
101			std::vector<std::streampos> framePos_;
102
103			bool needPos_;
104			bool needVel_;
105			bool needQuaternion_;
106	gezelter	1104	bool needAngMom_;
107			bool needCOMprops_;
108	tim	1024
109			const static int bufferSize = 4096;
110			char buffer[bufferSize];
111	chrisfen	721	};
112
113			} //end namespace oopse
114
115			#endif //IO_DUMPREADER_HPP