applications/sequentialProps/SequentialAnalyzer.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).
 */
#ifndef APPLICATIONS_SEQUENTIALPROPS_SEQUENTIALANALYZER_HPP
#define APPLICATIONS_SEQUENTIALPROPS_SEQUENTIALANALYZER_HPP

#include <string>
#include <vector>

#include "brains/SimInfo.hpp"
#include "brains/BlockSnapshotManager.hpp"

#include "primitives/StuntDouble.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"

namespace OpenMD {

  /**
   * @class SequentialAnalyzer SequentialAnalyzer.hpp "applications/sequentialProps/SequentialAnalyzer"
   * @brief Base class for Sequence Analyzer
   */
 
  class SequentialAnalyzer {
  public:
    SequentialAnalyzer(SimInfo* info, const std::string& filename) : 
      info_(info), currentSnapshot_(NULL), dumpFilename_(filename), 
      step_(1)  {}
    
    virtual ~SequentialAnalyzer(){ }    
    virtual void doSequence();

    void setOutputName(const std::string& filename) {
      outputFilename_ = filename;
    }

    const std::string& getOutputFileName() const {
      return outputFilename_;
    }

    void setStep(int step) {
      assert(step > 0);
      step_ = step;    
    }

    int getStep() { return step_; }

    const std::string& getSequenceType() const {
      return sequenceType_;
    }

    void setSequenceType(const std::string& type) {
      sequenceType_ = type;
    }

    void setExtraInfo(const std::string& extra) {
      extra_ = extra;
    }

  protected:
    virtual void preSequence() {}        
    virtual void postSequence() {}
    virtual void writeSequence();
    virtual void doFrame() = 0;

    SimInfo* info_;
    Snapshot* currentSnapshot_;
    std::string dumpFilename_;        
    std::string outputFilename_;
    int step_;
    int storageLayout_;
    std::vector<RealType> times_;
    std::vector<RealType> values_;
    std::string sequenceType_;
    std::string extra_;


  };
}
#endif
Revision:	2024
Committed:	Thu Oct 16 19:13:51 2014 UTC (10 years, 6 months ago) by gezelter
File size:	4011 byte(s)
Log Message:	Added Radial and Z-projected velocity autocorrelation functions Started to add SequentialProps program Mucking about with angular restraint potentials
#	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	#ifndef APPLICATIONS_SEQUENTIALPROPS_SEQUENTIALANALYZER_HPP
43	#define APPLICATIONS_SEQUENTIALPROPS_SEQUENTIALANALYZER_HPP
44
45	#include <string>
46	#include <vector>
47
48	#include "brains/SimInfo.hpp"
49	#include "brains/BlockSnapshotManager.hpp"
50
51	#include "primitives/StuntDouble.hpp"
52	#include "selection/SelectionEvaluator.hpp"
53	#include "selection/SelectionManager.hpp"
54
55	namespace OpenMD {
56
57	/**
58	* @class SequentialAnalyzer SequentialAnalyzer.hpp "applications/sequentialProps/SequentialAnalyzer"
59	* @brief Base class for Sequence Analyzer
60	*/
61
62	class SequentialAnalyzer {
63	public:
64	SequentialAnalyzer(SimInfo* info, const std::string& filename) :
65	info_(info), currentSnapshot_(NULL), dumpFilename_(filename),
66	step_(1) {}
67
68	virtual ~SequentialAnalyzer(){ }
69	virtual void doSequence();
70
71	void setOutputName(const std::string& filename) {
72	outputFilename_ = filename;
73	}
74
75	const std::string& getOutputFileName() const {
76	return outputFilename_;
77	}
78
79	void setStep(int step) {
80	assert(step > 0);
81	step_ = step;
82	}
83
84	int getStep() { return step_; }
85
86	const std::string& getSequenceType() const {
87	return sequenceType_;
88	}
89
90	void setSequenceType(const std::string& type) {
91	sequenceType_ = type;
92	}
93
94	void setExtraInfo(const std::string& extra) {
95	extra_ = extra;
96	}
97
98	protected:
99	virtual void preSequence() {}
100	virtual void postSequence() {}
101	virtual void writeSequence();
102	virtual void doFrame() = 0;
103
104	SimInfo* info_;
105	Snapshot* currentSnapshot_;
106	std::string dumpFilename_;
107	std::string outputFilename_;
108	int step_;
109	int storageLayout_;
110	std::vector<RealType> times_;
111	std::vector<RealType> values_;
112	std::string sequenceType_;
113	std::string extra_;
114
115
116	};
117	}
118	#endif