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, 24107 (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:	1794
Committed:	Thu Sep 6 19:44:06 2012 UTC (12 years, 7 months ago) by gezelter
File size:	4210 byte(s)
Log Message:	Merging some of the trunk changes back to the development branch, cleaning up a datastorage bug
#	User	Rev	Content
1	cli2	1360	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	cli2	1360	*/
42
43			/**
44			* @file RestReader.hpp
45			*/
46
47			#ifndef IO_RESTREADER_HPP
48			#define IO_RESTREADER_HPP
49
50	cli2	1407	#include <cstdio>
51			#include <string>
52			#include "brains/SimInfo.hpp"
53			#include "primitives/StuntDouble.hpp"
54	chrisfen	417
55	gezelter	1390	namespace OpenMD {
56	cli2	1360
57			/**
58			* @class RestReader RestReader.hpp "io/RestReader.hpp"
59			*/
60	cli2	1407	class RestReader {
61	cli2	1360	public:
62	cli2	1407	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	gezelter	1794	inFile_ = new std::ifstream(filename_.c_str(),
72			ifstream::in \| ifstream::binary);
73	cli2	1407
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			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	cli2	1360	protected:
112	cli2	1407	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	cli2	1360	private:
118	cli2	1407
119			SimInfo* info_;
120
121	cli2	1360	std::vector<Vector3d> all_pos_;
122	cli2	1407	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	chrisfen	417	};
132	cli2	1360
133	gezelter	1390	} //end namespace OpenMD
134	cli2	1360
135			#endif //IO_RESTREADER_HPP