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Comparing trunk/src/io/RestReader.hpp (file contents):
Revision 996 by chrisfen, Wed Jun 28 14:35:14 2006 UTC vs.
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC

# Line 1 | Line 1
1 < /*
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 < #ifndef IO_RESTREADER_HPP
42 < #define IO_RESTREADER_HPP
1 > /*
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 RestReader.hpp
44 > */
45 >
46 > #ifndef IO_RESTREADER_HPP
47 > #define IO_RESTREADER_HPP
48 >
49 > #include "io/DumpReader.hpp"
50  
51 < #define _LARGEFILE_SOURCE64
52 < #ifndef _FILE_OFFSET_BITS
53 < #define _FILE_OFFSET_BITS 64
54 < #endif
55 < #include <iostream>
56 < #include <fstream>
57 < #include <string>
58 < #include <stdio.h>
59 < #include <stdlib.h>
60 < #include <unistd.h>
61 < #include <sys/types.h>
62 < #include <sys/stat.h>
63 <
64 < #include "brains/SimInfo.hpp"
58 < #include "primitives/StuntDouble.hpp"
59 <
60 < namespace oopse {
61 <    
62 <
63 <  /**
64 <   * @class RestReader RestReader.hpp "io/RestReader.hpp"
65 <   * @for extra file reading when using thermodynamic integration
66 <   */
67 <  class RestReader {
68 <    
69 <  public:
70 <    RestReader( SimInfo* theInfo );
71 <    ~RestReader();
72 <    
73 <    void readIdealCrystal();
74 <    void readZangle();
75 <    void zeroZangle();
76 <    
77 <  private:
78 <    char* parseIdealLine(char* readLine, StuntDouble* sd);
79 <    std::string angFile;
80 <    std::string idealName;
81 <    std::istream* inIdealFile;
82 <    std::istream* inAngFile;
83 <
84 <    RealType angleTransfer;
85 <    SimInfo *info_;
51 > namespace oopse {
52 >
53 >  /**
54 >   * @class RestReader RestReader.hpp "io/RestReader.hpp"
55 >   */
56 >  class RestReader : public DumpReader {
57 >  public:
58 >    RestReader(SimInfo* info, const std::string &filename) : DumpReader(info, filename){}
59 >    void readReferenceStructure();
60 >  protected:
61 >    virtual void parseDumpLine(const std::string&);  
62 >    virtual void readFrameProperties(std::istream& inputStream);
63 >  private:
64 >    std::vector<Vector3d> all_pos_;
65    };
66 <
67 < } //end namespace oopse
68 < #endif
66 >
67 > }      //end namespace oopse
68 >
69 > #endif //IO_RESTREADER_HPP

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