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

Comparing:
trunk/src/io/RestReader.hpp (file contents), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/io/RestReader.hpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 1 | Line 1
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
19	<	*    notice, this list of conditions and the following disclaimer.
20	<	*
21	<	* 3. Redistributions in binary form must reproduce the above copyright
22	<	*    notice, this list of conditions and the following disclaimer in the
23	<	*    documentation and/or other materials provided with the
24	<	*    distribution.
25	<	*
26	<	* This software is provided "AS IS," without a warranty of any
27	<	* 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
33	<	* derivatives. In no event will the University of Notre Dame or its
34	<	* licensors be liable for any lost revenue, profit or data, or for
35	<	* 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
38	<	* University of Notre Dame has been advised of the possibility of
39	<	* such damages.
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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, 234107 (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		/**
#	Line 46 | Line 47
47		#ifndef IO_RESTREADER_HPP
48		#define IO_RESTREADER_HPP
49
50	<	#include "io/DumpReader.hpp"
50	>	#include <cstdio>
51	>	#include <string>
52	>	#include "brains/SimInfo.hpp"
53	>	#include "primitives/StuntDouble.hpp"
54
55	<	namespace oopse {
55	>	namespace OpenMD {
56
57		/**
58		* @class RestReader RestReader.hpp "io/RestReader.hpp"
59		*/
60	<	class RestReader : public DumpReader {
60	>	class RestReader {
61		public:
62	<	RestReader(SimInfo* info, const std::string &filename) : DumpReader(info, filename){}
63	<	void readReferenceStructure();
62	>	RestReader(SimInfo* info, const std::string &filename,
63	>	std::vector<int> stuntDoubleIndex)
64	>	: info_(info), filename_(filename), stuntDoubleIndex_(stuntDoubleIndex) {
65	>	#ifdef IS_MPI
66	>
67	>	if (worldRank == 0) {
68	>	#endif
69	>
70	>	inFile_ = new std::ifstream(filename_.c_str(),
71	>	ifstream::in | ifstream::binary);
72	>
73	>	if (inFile_->fail()) {
74	>	sprintf(painCave.errMsg,
75	>	"RestReader: Cannot open file: %s\n",
76	>	filename_.c_str());
77	>	painCave.isFatal = 1;
78	>	simError();
79	>	}
80	>
81	>	#ifdef IS_MPI
82	>
83	>	}
84	>
85	>	strcpy(checkPointMsg, "Reference file opened for reading successfully.");
86	>	errorCheckPoint();
87	>
88	>	#endif
89	>
90	>	return;
91	>	}
92	>
93	>	void readReferenceStructure(void);
94	>
95	>	~RestReader(){
96	>	#ifdef IS_MPI
97	>	if (worldRank == 0){
98	>	#endif
99	>
100	>	delete inFile_;
101	>
102	>	#ifdef IS_MPI
103	>	}
104	>
105	>	strcpy(checkPointMsg, "Reference file closed successfully.");
106	>	errorCheckPoint();
107	>	#endif
108	>	}
109	>
110		protected:
111	<	virtual void parseDumpLine(const std::string&);
112	<	virtual void readFrameProperties(std::istream& inputStream);
111	>	void parseDumpLine(const std::string& line);
112	>	void readStuntDoubles(std::istream& inpuStream);
113	>	void readFrameProperties(std::istream& inputStream);
114	>	void scanFile(void);
115	>	void readSet(void);
116		private:
117	+
118	+	SimInfo* info_;
119	+
120		std::vector<Vector3d> all_pos_;
121	+	std::vector<int> stuntDoubleIndex_;
122	+
123	+	std::istream* inFile_;
124	+	std::string filename_;
125	+
126	+	std::streampos framePos_;
127	+
128	+	const static int bufferSize = 4096;
129	+	char buffer[bufferSize];
130		};
131
132	<	}      //end namespace oopse
132	>	}      //end namespace OpenMD
133
134		#endif //IO_RESTREADER_HPP

Comparing:
trunk/src/io/RestReader.hpp (property svn:keywords), Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
branches/development/src/io/RestReader.hpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

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