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Comparing trunk/src/io/DumpWriter.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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. 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 + * 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   #ifndef IO_DUMPWRITER_HPP
# Line 52 | Line 53
53   #include <string.h>
54   #include <stdio.h>
55   #include <stdlib.h>
56 < #include <unistd.h>
56 > // #include <unistd.h>
57   #include <sys/types.h>
58   #include <sys/stat.h>
59  
# Line 61 | Line 62
62   #include "brains/Thermo.hpp"
63   #include "primitives/StuntDouble.hpp"
64  
65 < namespace oopse {
65 > namespace OpenMD {
66  
67    /**
68     * @class DumpWriter DumpWriter.hpp "io/DumpWriter.hpp"
# Line 72 | Line 73 | namespace oopse {
73    public:
74      DumpWriter(SimInfo* info);
75      DumpWriter(SimInfo* info, const std::string& filename);
76 +    DumpWriter(SimInfo* info, const std::string& filename,  bool writeDumpFile);
77      ~DumpWriter();
78  
79      void writeDumpAndEor();
80      void writeDump();
81      void writeEor();
82 <        
82 >    
83    private:  
84          
85      void writeFrame(std::ostream& os);
86 <    void writeCommentLine(std::ostream& os, Snapshot* s);
86 >    void writeFrameProperties(std::ostream& os, Snapshot* s);
87 >    std::string prepareDumpLine(StuntDouble* sd);
88 >    std::string prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex);
89 >    std::ostream* createOStream(const std::string& filename);
90 >    void writeClosing(std::ostream& os);
91 >    
92      SimInfo* info_;
93      std::string filename_;
94 <    std::ofstream dumpFile_;
94 >    std::ostream* dumpFile_;
95      std::string eorFilename_;
96 +    bool needCompression_;
97 +    bool needForceVector_;
98 +    bool needParticlePot_;
99 +    bool needFlucQ_;
100 +    bool needElectricField_;
101 +    bool doSiteData_;
102 +    bool createDumpFile_;
103    };
104  
105   }

Comparing trunk/src/io/DumpWriter.hpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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