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Comparing trunk/src/io/DumpReader.hpp (file contents):
Revision 1024 by tim, Wed Aug 30 18:42:29 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 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 < */
1 > /*
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 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 > * [4]  Vardeman & Gezelter, in progress (2009).                        
40 > */
41    
42   /**
43   * @file DumpReader.hpp
# Line 54 | Line 54
54   #include <string>
55   #include "brains/SimInfo.hpp"
56   #include "primitives/StuntDouble.hpp"
57 < namespace oopse {
57 > namespace OpenMD {
58  
59    /**
60     * @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
# Line 66 | Line 66 | namespace oopse {
66      DumpReader(SimInfo* info, const std::string & filename);
67      //DumpReader(SimInfo * info, istream & is);
68  
69 <    ~DumpReader();
69 >    virtual ~DumpReader();
70  
71      /** Returns the number of frames in the dump file*/
72      int getNFrames();
73  
74 +    void setNeedCOMprops(bool ncp) {
75 +      needCOMprops_ = ncp;
76 +    }
77          
78 <    void readFrame(int whichFrame);
78 >    virtual void readFrame(int whichFrame);
79  
80 <  private:
80 >  protected:
81  
82      void scanFile();
83  
84      void readSet(int whichFrame);
85  
86 <    void parseDumpLine(const std::string&);
86 >    virtual void parseDumpLine(const std::string&);
87  
88 <    void readFrameProperties(std::istream& inputStream);
88 >    virtual void readFrameProperties(std::istream& inputStream);
89  
90 <    void readStuntDoubles(std::istream& inputStream);
88 <                  
90 >    void readStuntDoubles(std::istream& inputStream);                  
91          
92      SimInfo* info_;
93  
# Line 101 | Line 103 | namespace oopse {
103      bool needPos_;
104      bool needVel_;
105      bool needQuaternion_;
106 <    bool needAngMom_;
106 >    bool needAngMom_;
107 >    bool needCOMprops_;
108  
109      const static int bufferSize = 4096;
110      char buffer[bufferSize];
111    };
112  
113 < }      //end namespace oopse
113 > }      //end namespace OpenMD
114  
115   #endif //IO_DUMPREADER_HPP

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