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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 1752 by gezelter, Sun Jun 10 14:05:02 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	+	/**
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	<	*/
58	<
59	<	#ifndef IO_DUMPREADER_HPP
60	<	#define IO_DUMPREADER_HPP
61	<
62	<	#include <cstdio>
63	<	#include <string>
64	<	#include "brains/SimInfo.hpp"
65	<	#include "primitives/StuntDouble.hpp"
66	<	namespace oopse {
67	<
68	<	/**
69	<	* @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
70	<	* @todo get rid of more junk code from DumpReader
71	<	*/
72	<	class DumpReader {
73	<	public:
74	<
75	<	DumpReader(SimInfo* info, const std::string & filename);
76	<	//DumpReader(SimInfo * info, istream & is);
77	<
78	<	~DumpReader();
79	<
80	<	/** Returns the number of frames in the dump file*/
81	<	int getNFrames();
82	<
83	<
84	<	void readFrame(int whichFrame);
85	<
86	<	private:
87	<
88	<	void scanFile();
89	<
90	<	void readSet(int whichFrame);
91	<
92	<	void parseDumpLine(char *line, StuntDouble* integrableObject);
93	<
94	<	void parseCommentLine(char* line, Snapshot* s);
95	<
96	<
97	<	#ifdef IS_MPI
98	<
99	<	void anonymousNodeDie(void);
100	<	void nodeZeroError(void);
101	<
102	<	#endif
103	<	// the maximum length of a typical MPI package is 15k
104	<	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_;
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	>	void readSet(int whichFrame);
85	>	virtual void parseDumpLine(const std::string&);
86	>	virtual void parseSiteLine(const std::string&);
87	>	virtual void readFrameProperties(std::istream& inputStream);
88	>	void readStuntDoubles(std::istream& inputStream);
89	>	void readSiteData(std::istream& inputStream);
90	>
91	>	SimInfo* info_;
92	>
93	>	std::string filename_;
94	>	bool isScanned_;
95	>
96	>	int nframes_;
97	>
98	>	std::istream* inFile_;
99	>
100	>	std::vector<std::streampos> framePos_;
101	>
102	>	bool needPos_;
103	>	bool needVel_;
104	>	bool needQuaternion_;
105		bool needAngMom_;
106	<	};
106	>	bool needCOMprops_;
107
108	<	}      //end namespace oopse
109	<
110	<	#endif //IO_DUMPREADER_HPP
108	>	const static int bufferSize = 4096;
109	>	char buffer[bufferSize];
110	>	};
111	>
112	>	}      //end namespace OpenMD
113	>
114	>	#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 1752 by gezelter, Sun Jun 10 14:05:02 2012 UTC

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