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root/OpenMD/branches/development/src/io/DumpReader.hpp

Comparing:
trunk/src/io/DumpReader.hpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpReader.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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	+	/**
44	+	* @file DumpReader.hpp
45	+	* @author tlin
46	+	* @date 11/15/2004
47	+	* @time 09:25am
48	+	* @version 2.0
49	+	*/
50
51	<	/**
52	<	* @file DumpReader.hpp
53	<	* @author tlin
54	<	* @date 11/15/2004
55	<	* @time 09:25am
56	<	* @version 2.0
57	<	*/
51	>	#ifndef IO_DUMPREADER_HPP
52	>	#define IO_DUMPREADER_HPP
53	>
54	>	#include <cstdio>
55	>	#include <string>
56	>	#include "brains/SimInfo.hpp"
57	>	#include "primitives/StuntDouble.hpp"
58	>	namespace OpenMD {
59	>
60	>	/**
61	>	* @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
62	>	* @todo get rid of more junk code from DumpReader
63	>	*/
64	>	class DumpReader {
65	>	public:
66	>
67	>	DumpReader(SimInfo* info, const std::string & filename);
68	>	//DumpReader(SimInfo * info, istream & is);
69	>
70	>	virtual ~DumpReader();
71	>
72	>	/** Returns the number of frames in the dump file*/
73	>	int getNFrames();
74	>
75	>	void setNeedCOMprops(bool ncp) {
76	>	needCOMprops_ = ncp;
77	>	}
78	>
79	>	virtual void readFrame(int whichFrame);
80	>
81	>	protected:
82	>
83	>	void scanFile();
84	>
85	>	void readSet(int whichFrame);
86	>
87	>	virtual void parseDumpLine(const std::string&);
88	>
89	>	virtual void readFrameProperties(std::istream& inputStream);
90
91	<	#ifndef IO_DUMPREADER_HPP
92	<	#define IO_DUMPREADER_HPP
93	<
94	<	#include <cstdio>
95	<	#include <string>
96	<	#include "brains/SimInfo.hpp"
97	<	#include "primitives/StuntDouble.hpp"
98	<	namespace oopse {
99	<
100	<	/**
101	<	* @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
102	<	* @todo get rid of more junk code from DumpReader
103	<	*/
104	<	class DumpReader {
105	<	public:
106	<
66	<	DumpReader(SimInfo* info, const std::string & filename);
67	<	//DumpReader(SimInfo * info, istream & is);
68	<
69	<	~DumpReader();
70	<
71	<	/** Returns the number of frames in the dump file*/
72	<	int getNFrames();
73	<
74	<
75	<	void readFrame(int whichFrame);
76	<
77	<	private:
78	<
79	<	void scanFile();
80	<
81	<	void readSet(int whichFrame);
82	<
83	<	void parseDumpLine(char *line, StuntDouble* integrableObject);
84	<
85	<	void parseCommentLine(char* line, Snapshot* s);
86	<
87	<
88	<	#ifdef IS_MPI
89	<
90	<	void anonymousNodeDie(void);
91	<	void nodeZeroError(void);
92	<
93	<	#endif
94	<	// the maximum length of a typical MPI package is 15k
95	<	const static int maxBufferSize = 8192;
96	<
97	<	SimInfo* info_;
98	<
99	<	std::string filename_;
100	<	bool isScanned_;
101	<
102	<	int nframes_;
103	<
104	<	FILE* inFile_;
105	<	std::vector<fpos_t*> framePos_;
106	<
107	<	bool needPos_;
108	<	bool needVel_;
109	<	bool needQuaternion_;
91	>	void readStuntDoubles(std::istream& inputStream);
92	>
93	>	SimInfo* info_;
94	>
95	>	std::string filename_;
96	>	bool isScanned_;
97	>
98	>	int nframes_;
99	>
100	>	std::istream* inFile_;
101	>
102	>	std::vector<std::streampos> framePos_;
103	>
104	>	bool needPos_;
105	>	bool needVel_;
106	>	bool needQuaternion_;
107		bool needAngMom_;
108	<	};
108	>	bool needCOMprops_;
109
110	<	}      //end namespace oopse
111	<
112	<	#endif //IO_DUMPREADER_HPP
110	>	const static int bufferSize = 4096;
111	>	char buffer[bufferSize];
112	>	};
113	>
114	>	}      //end namespace OpenMD
115	>
116	>	#endif //IO_DUMPREADER_HPP

Comparing:
trunk/src/io/DumpReader.hpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/io/DumpReader.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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