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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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/** |
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* @file DumpReader.hpp |
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* @author tlin |
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* @date 11/15/2004 |
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* @time 09:25am |
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* @version 2.0 |
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*/ |
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|
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#ifndef IO_DUMPREADER_HPP |
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#define IO_DUMPREADER_HPP |
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|
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#include <cstdio> |
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#include <string> |
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#include "brains/SimInfo.hpp" |
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#include "primitives/StuntDouble.hpp" |
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namespace oopse { |
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|
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/** |
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* @class DumpReader DumpReader.hpp "io/DumpReader.hpp" |
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* @todo get rid of more junk code from DumpReader |
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*/ |
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class DumpReader { |
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public: |
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|
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DumpReader(SimInfo* info, const std::string & filename); |
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//DumpReader(SimInfo * info, istream & is); |
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|
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~DumpReader(); |
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|
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/** Returns the number of frames in the dump file*/ |
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int getNFrames(); |
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|
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|
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void readFrame(int whichFrame); |
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|
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private: |
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|
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void scanFile(); |
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|
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void readSet(int whichFrame); |
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|
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void parseDumpLine(char *line, StuntDouble* integrableObject); |
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|
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void parseCommentLine(char* line, Snapshot* s); |
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|
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|
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#ifdef IS_MPI |
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|
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void anonymousNodeDie(void); |
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void nodeZeroError(void); |
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|
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#endif |
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// the maximum length of a typical MPI package is 15k |
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const static int maxBufferSize = 8192; |
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|
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SimInfo* info_; |
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|
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std::string filename_; |
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bool isScanned_; |
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|
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int nframes_; |
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|
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FILE* inFile_; |
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std::vector<fpos_t*> framePos_; |
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}; |
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|
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} //end namespace oopse |
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|
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#endif //IO_DUMPREADER_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," |
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> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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> |
* |
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* 2. Redistributions of source code must retain the above copyright |
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> |
* notice, this list of conditions and the following disclaimer. |
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> |
* |
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> |
* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* notice, this list of conditions and the following disclaimer in the |
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> |
* documentation and/or other materials provided with the |
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> |
* distribution. |
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> |
* |
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> |
* This software is provided "AS IS," without a warranty of any |
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> |
* 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 |
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> |
* derivatives. In no event will the University of Notre Dame or its |
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> |
* licensors be liable for any lost revenue, profit or data, or for |
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> |
* 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 |
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> |
* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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/** |
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* @file DumpReader.hpp |
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* @author tlin |
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* @date 11/15/2004 |
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* @time 09:25am |
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* @version 2.0 |
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*/ |
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|
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#ifndef IO_DUMPREADER_HPP |
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#define IO_DUMPREADER_HPP |
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|
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#include <cstdio> |
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#include <string> |
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#include "brains/SimInfo.hpp" |
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#include "primitives/StuntDouble.hpp" |
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namespace oopse { |
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|
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/** |
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* @class DumpReader DumpReader.hpp "io/DumpReader.hpp" |
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* @todo get rid of more junk code from DumpReader |
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*/ |
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class DumpReader { |
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public: |
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|
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DumpReader(SimInfo* info, const std::string & filename); |
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//DumpReader(SimInfo * info, istream & is); |
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|
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~DumpReader(); |
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|
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/** Returns the number of frames in the dump file*/ |
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int getNFrames(); |
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|
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|
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void readFrame(int whichFrame); |
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|
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private: |
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|
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void scanFile(); |
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|
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void readSet(int whichFrame); |
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|
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void parseDumpLine(char *line, StuntDouble* integrableObject); |
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|
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void parseCommentLine(char* line, Snapshot* s); |
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|
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|
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#ifdef IS_MPI |
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|
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void anonymousNodeDie(void); |
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void nodeZeroError(void); |
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|
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#endif |
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// the maximum length of a typical MPI package is 15k |
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const static int maxBufferSize = 8192; |
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|
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SimInfo* info_; |
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|
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std::string filename_; |
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bool isScanned_; |
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|
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int nframes_; |
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|
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std::istream* inFile_; |
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|
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std::vector<std::streampos> framePos_; |
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|
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bool needPos_; |
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bool needVel_; |
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bool needQuaternion_; |
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bool needAngMom_; |
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}; |
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|
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} //end namespace oopse |
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|
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#endif //IO_DUMPREADER_HPP |
