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Comparing trunk/src/io/RestReader.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 UTC

# Line 1 | Line 1
1 < /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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 < #ifndef IO_RESTREADER_HPP
33 < #define IO_RESTREADER_HPP
34 <
35 < #define _LARGEFILE_SOURCE64
36 < #ifndef _FILE_OFFSET_BITS
37 < #define _FILE_OFFSET_BITS 64
38 < #endif
39 < #include <iostream>
40 < #include <fstream>
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]  Vardeman & Gezelter, in progress (2009).                        
40 > */
41 >  
42 > /**
43 > * @file RestReader.hpp
44 > */
45 >
46 > #ifndef IO_RESTREADER_HPP
47 > #define IO_RESTREADER_HPP
48 >
49 > #include <cstdio>
50   #include <string>
51 – #include <stdio.h>
52 – #include <stdlib.h>
53 – #include <unistd.h>
54 – #include <sys/types.h>
55 – #include <sys/stat.h>
56 –
51   #include "brains/SimInfo.hpp"
52   #include "primitives/StuntDouble.hpp"
53  
54 < namespace oopse {
55 <    
54 > namespace OpenMD {
55 >
56 >  /**
57 >   * @class RestReader RestReader.hpp "io/RestReader.hpp"
58 >   */
59 >  class RestReader {
60 >  public:
61 >    RestReader(SimInfo* info, const std::string &filename,
62 >                           std::vector<int> stuntDoubleIndex)
63 >      : info_(info), filename_(filename){
64 >      stuntDoubleIndex_ = stuntDoubleIndex;
65 > #ifdef IS_MPI
66 >      
67 >      if (worldRank == 0) {
68 > #endif
69 >        
70 >        inFile_ = new std::ifstream(filename_.c_str());
71 >        
72 >        if (inFile_->fail()) {
73 >          sprintf(painCave.errMsg,
74 >                  "RestReader: Cannot open file: %s\n",
75 >                  filename_.c_str());
76 >          painCave.isFatal = 1;
77 >          simError();
78 >        }
79 >        
80 > #ifdef IS_MPI
81 >        
82 >      }
83 >      
84 >      strcpy(checkPointMsg, "Reference file opened for reading successfully.");
85 >      errorCheckPoint();
86 >      
87 > #endif
88 >      
89 >      return;
90 >    }
91  
92 <  /**
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 <    char *idealName;
80 <    FILE *inAngFile;
81 <    FILE *inIdealFile;
82 <    std::string inAngFileName;
83 <    std::string inIdealFileName;
84 <    bool isScanned;
85 <    
86 <    RealType angleTransfer;
87 <    std::vector<fpos_t*> framePos;
88 <    SimInfo *info_;
89 <  };
92 >    void readReferenceStructure(void);
93  
94 < } //end namespace oopse
94 >    ~RestReader(){
95 > #ifdef IS_MPI
96 >      if (worldRank == 0){
97 > #endif
98 >        
99 >        delete inFile_;
100 >        
101 > #ifdef IS_MPI      
102 >      }
103 >      
104 >      strcpy(checkPointMsg, "Reference file closed successfully.");
105 >      errorCheckPoint();
106   #endif
107 +    }
108 +    
109 +  protected:
110 +    void parseDumpLine(const std::string& line);
111 +    void readStuntDoubles(std::istream& inpuStream);
112 +    void readFrameProperties(std::istream& inputStream);
113 +    void scanFile(void);
114 +    void readSet(void);
115 +  private:
116 +
117 +    SimInfo* info_;
118 +
119 +    std::vector<Vector3d> all_pos_;
120 +    std::vector<int> stuntDoubleIndex_;
121 +
122 +    std::istream* inFile_;
123 +    std::string filename_;
124 +
125 +    std::streampos framePos_;
126 +
127 +    const static int bufferSize = 4096;
128 +    char buffer[bufferSize];
129 +  };
130 +
131 + }      //end namespace OpenMD
132 +
133 + #endif //IO_RESTREADER_HPP

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