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

Comparing:
trunk/src/io/DumpReader.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/io/DumpReader.hpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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. 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	+	* @version 2.0
48	+	*/
49
50	<	/**
51	<	* @file DumpReader.hpp
52	<	* @author tlin
53	<	* @date 11/15/2004
54	<	* @time 09:25am
55	<	* @version 2.0
56	<	*/
50	>	#ifndef IO_DUMPREADER_HPP
51	>	#define IO_DUMPREADER_HPP
52	>
53	>	#include <cstdio>
54	>	#include <string>
55	>	#include "brains/SimInfo.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	namespace OpenMD {
58	>
59	>	/**
60	>	* @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
61	>	* @todo get rid of more junk code from DumpReader
62	>	*/
63	>	class DumpReader {
64	>	public:
65	>
66	>	DumpReader(SimInfo* info, const std::string & filename);
67	>	//DumpReader(SimInfo * info, istream & is);
68	>
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	>	virtual void readFrame(int whichFrame);
79	>
80	>	protected:
81	>
82	>	void scanFile();
83	>	void readSet(int whichFrame);
84	>	virtual void parseDumpLine(const std::string&);
85	>	virtual void parseSiteLine(const std::string&);
86	>	virtual void readFrameProperties(std::istream& inputStream);
87	>	void readStuntDoubles(std::istream& inputStream);
88	>	void readSiteData(std::istream& inputStream);
89	>
90	>	SimInfo* info_;
91	>
92	>	std::string filename_;
93	>	bool isScanned_;
94	>
95	>	int nframes_;
96	>
97	>	std::istream* inFile_;
98	>
99	>	std::vector<std::streampos> framePos_;
100	>
101	>	bool needPos_;
102	>	bool needVel_;
103	>	bool needQuaternion_;
104	>	bool needAngMom_;
105	>	bool needCOMprops_;
106
107	<	#ifndef IO_DUMPREADER_HPP
108	<	#define IO_DUMPREADER_HPP
109	<
110	<	#include <cstdio>
111	<	#include <string>
112	<	#include "brains/SimInfo.hpp"
113	<	#include "primitives/StuntDouble.hpp"
57	<	namespace oopse {
58	<
59	<	/**
60	<	* @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
61	<	* @todo get rid of more junk code from DumpReader
62	<	*/
63	<	class DumpReader {
64	<	public:
65	<
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	<
108	<	}      //end namespace oopse
109	<
110	<	#endif //IO_DUMPREADER_HPP
107	>	const static int bufferSize = 4096;
108	>	char buffer[bufferSize];
109	>	};
110	>
111	>	}      //end namespace OpenMD
112	>
113	>	#endif //IO_DUMPREADER_HPP

Comparing:
trunk/src/io/DumpReader.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/io/DumpReader.hpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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