src/io/RestReader.hpp

/* 
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. 
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */ 
  
/** 
 * @file RestReader.hpp 
 */ 
 
#ifndef IO_RESTREADER_HPP 
#define IO_RESTREADER_HPP 
 
#include <cstdio>
#include <string>
#include "brains/SimInfo.hpp"
#include "primitives/StuntDouble.hpp"

namespace OpenMD { 
 
  /** 
   * @class RestReader RestReader.hpp "io/RestReader.hpp" 
   */ 
  class RestReader { 
  public: 
    RestReader(SimInfo* info, const std::string &filename, 
                           std::vector<int> stuntDoubleIndex) 
      : info_(info), filename_(filename), stuntDoubleIndex_(stuntDoubleIndex) {
#ifdef IS_MPI 
      
      if (worldRank == 0) { 
#endif 
        
        inFile_ = new std::ifstream(filename_.c_str(),
                                    ifstream::in | ifstream::binary); 
        
        if (inFile_->fail()) { 
          sprintf(painCave.errMsg, 
                  "RestReader: Cannot open file: %s\n", 
                  filename_.c_str()); 
          painCave.isFatal = 1; 
          simError(); 
        } 
        
#ifdef IS_MPI 
        
      } 
      
      strcpy(checkPointMsg, "Reference file opened for reading successfully."); 
      errorCheckPoint(); 
      
#endif 
      
      return;
    }

    void readReferenceStructure(void);

    ~RestReader(){
#ifdef IS_MPI
      if (worldRank == 0){
#endif 
        
        delete inFile_;
        
#ifdef IS_MPI       
      } 
      
      strcpy(checkPointMsg, "Reference file closed successfully."); 
      errorCheckPoint();
#endif
    }
    
  protected: 
    void parseDumpLine(const std::string& line);
    void readStuntDoubles(std::istream& inpuStream);
    void readFrameProperties(std::istream& inputStream);
    void scanFile(void);
    void readSet(void);
  private: 

    SimInfo* info_;

    std::vector<Vector3d> all_pos_;
    std::vector<int> stuntDoubleIndex_;

    std::istream* inFile_;
    std::string filename_;

    std::streampos framePos_;

    const static int bufferSize = 4096;
    char buffer[bufferSize];
  };
 
}      //end namespace OpenMD 
 
#endif //IO_RESTREADER_HPP 
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	4205 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
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. 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	/**
44	* @file RestReader.hpp
45	*/
46
47	#ifndef IO_RESTREADER_HPP
48	#define IO_RESTREADER_HPP
49
50	#include <cstdio>
51	#include <string>
52	#include "brains/SimInfo.hpp"
53	#include "primitives/StuntDouble.hpp"
54
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), 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	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 OpenMD
133
134	#endif //IO_RESTREADER_HPP