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

Comparing:
trunk/src/io/RestReader.hpp (file contents), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/io/RestReader.hpp (file contents), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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
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	<	#ifndef IO_RESTREADER_HPP
33	<	#define IO_RESTREADER_HPP
34	<
35	<	#define _LARGEFILE_SOURCE64
36	<	#ifndef _FILE_OFFSET_BITS
37	<	#define _FILE_OFFSET_BITS 64
38	<	#endif
39	<	#include <iostream>
40	<	#include <fstream>
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 RestReader.hpp
45	>	*/
46	>
47	>	#ifndef IO_RESTREADER_HPP
48	>	#define IO_RESTREADER_HPP
49	>
50	>	#include <cstdio>
51		#include <string>
51	–	#include <stdio.h>
52	–	#include <stdlib.h>
53	–	#include <unistd.h>
54	–	#include <sys/types.h>
55	–	#include <sys/stat.h>
56	–
52		#include "brains/SimInfo.hpp"
53		#include "primitives/StuntDouble.hpp"
54
55	<	namespace oopse {
56	<
55	>	namespace OpenMD {
56	>
57	>	/**
58	>	* @class RestReader RestReader.hpp "io/RestReader.hpp"
59	>	*/
60	>	class RestReader {
61	>	public:
62	>	RestReader(SimInfo* info, const std::string &filename,
63	>	std::vector<int> stuntDoubleIndex)
64	>	: info_(info), filename_(filename){
65	>	stuntDoubleIndex_ = stuntDoubleIndex;
66	>	#ifdef IS_MPI
67	>
68	>	if (worldRank == 0) {
69	>	#endif
70	>
71	>	inFile_ = new std::ifstream(filename_.c_str(),
72	>	ifstream::in | ifstream::binary);
73	>
74	>	if (inFile_->fail()) {
75	>	sprintf(painCave.errMsg,
76	>	"RestReader: Cannot open file: %s\n",
77	>	filename_.c_str());
78	>	painCave.isFatal = 1;
79	>	simError();
80	>	}
81	>
82	>	#ifdef IS_MPI
83	>
84	>	}
85	>
86	>	strcpy(checkPointMsg, "Reference file opened for reading successfully.");
87	>	errorCheckPoint();
88	>
89	>	#endif
90	>
91	>	return;
92	>	}
93
94	<	/**
95	<	* @class RestReader RestReader.hpp "io/RestReader.hpp"
96	<	* @for extra file reading when using thermodynamic integration
97	<	*/
98	<	class RestReader {
94	>	void readReferenceStructure(void);
95	>
96	>	~RestReader(){
97	>	#ifdef IS_MPI
98	>	if (worldRank == 0){
99	>	#endif
100	>
101	>	delete inFile_;
102	>
103	>	#ifdef IS_MPI
104	>	}
105	>
106	>	strcpy(checkPointMsg, "Reference file closed successfully.");
107	>	errorCheckPoint();
108	>	#endif
109	>	}
110
111	<	public:
112	<	RestReader( SimInfo* theInfo );
113	<	~RestReader();
114	<
115	<	void readIdealCrystal();
116	<	void readZangle();
117	<	void zeroZangle();
76	<
77	<	private:
78	<	char* parseIdealLine(char* readLine, StuntDouble* sd);
79	<	char *idealName;
80	<	FILE *inAngFile;
81	<	FILE *inIdealFile;
82	<	std::string inAngFileName;
83	<	std::string inIdealFileName;
84	<	bool isScanned;
85	<
86	<	double angleTransfer;
87	<	std::vector<fpos_t*> framePos;
88	<	SimInfo *info_;
89	<	};
111	>	protected:
112	>	void parseDumpLine(const std::string& line);
113	>	void readStuntDoubles(std::istream& inpuStream);
114	>	void readFrameProperties(std::istream& inputStream);
115	>	void scanFile(void);
116	>	void readSet(void);
117	>	private:
118
119	<	} //end namespace oopse
120	<	#endif
119	>	SimInfo* info_;
120	>
121	>	std::vector<Vector3d> all_pos_;
122	>	std::vector<int> stuntDoubleIndex_;
123	>
124	>	std::istream* inFile_;
125	>	std::string filename_;
126	>
127	>	std::streampos framePos_;
128	>
129	>	const static int bufferSize = 4096;
130	>	char buffer[bufferSize];
131	>	};
132	>
133	>	}      //end namespace OpenMD
134	>
135	>	#endif //IO_RESTREADER_HPP

Comparing:
trunk/src/io/RestReader.hpp (property svn:keywords), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/io/RestReader.hpp (property svn:keywords), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

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