applications/staticProps/SurfaceDiffusion.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).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *  Created by Joseph R. Michalka on 06/13/12.
 *  @author  Joseph R. Michalka
 *  @version $Id: SurfaceDisruption.hpp 1665 2011-11-22 20:38:56Z gezelter $
 *
 */
#ifndef APPLICATIONS_STATICPROPS_SURFACEDIFFUSION_HPP
#define APPLICATIONS_STATICPROPS_SURFACEDIFFUSION_HPP

#include <string>
#include <vector>
#include <fstream>
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "utils/NumericConstant.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"

namespace OpenMD {
  
  class SurfaceDiffusion: public StaticAnalyser {
    
  public:
    SurfaceDiffusion(SimInfo* info, const std::string& filename, const std::string& sele, RealType len);
    virtual ~SurfaceDiffusion();
    
    virtual void process();
    
  private:
    
    double round(double r);
    void solventAccessible();
    void mobileAtomsFirst();
    void mobileAtomsLast();
    void mobileAtoms();
    void positionCorrelation();

    Snapshot* currentSnapshot_;
    
    int nProcessed_;
    std::string selectionScript_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan1_;
  
    string filename_;
    int bins_; 
    int selectionCount_;
    double singleMoveDistance_;
    int frames_;
    bool doSolvent_;


    //All positions of all frames of selected indices
    //positions_[0][i]
    // First particle at frame i
    std::vector< std::vector<Vector3d> > positions_;
    std::vector< std::vector<Vector3d> > positions2_;

    //mobility of particle i at time j
    // moBool[i][j]
    // moBool.resize(selectionCount_);
    // for(){
    //  moBool[i].resize(frames);
    // }
    std::vector< std::vector<bool> > moBool_;
    std::vector< std::vector<bool> > moBool2_;

    std::vector< std::vector<StuntDouble*> > gridSD_;
    std::vector<StuntDouble*> gridHighZ_;
    std::vector<StuntDouble*> gridLowZ_;
    std::vector<StuntDouble*> forIndex_;
    std::vector<Vector3d> firstPosition_;
    std::vector<Vector3d> lastPosition_;


    std::vector<int> SAIndices_;
    std::vector<int> mobileIndices_;
    std::vector<int> indices_;
    std::vector<int> count_;

    std::vector<RealType> xHist_;
    std::vector<RealType> yHist_;
    std::vector<RealType> rHist_;

    RealType minDistance_;
    RealType probe_;
  };
  
}
#endif


Revision:	2032
Committed:	Fri Oct 31 18:57:19 2014 UTC (10 years, 6 months ago) by jmichalk
File size:	4455 byte(s)
Log Message:	Forgot to svn add the files. Additionally, examined the files where changes were committed that I didn't realize were going to be changed. Primary one to examine SimplePreprocessor, bufferSize=8192 instead of 1024... everything else was commented cerr/cout or line spacing issues
#	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, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	* Created by Joseph R. Michalka on 06/13/12.
42	* @author Joseph R. Michalka
43	* @version $Id: SurfaceDisruption.hpp 1665 2011-11-22 20:38:56Z gezelter $
44	*
45	*/
46	#ifndef APPLICATIONS_STATICPROPS_SURFACEDIFFUSION_HPP
47	#define APPLICATIONS_STATICPROPS_SURFACEDIFFUSION_HPP
48
49	#include <string>
50	#include <vector>
51	#include <fstream>
52	#include "selection/SelectionEvaluator.hpp"
53	#include "selection/SelectionManager.hpp"
54	#include "utils/NumericConstant.hpp"
55	#include "applications/staticProps/StaticAnalyser.hpp"
56
57	namespace OpenMD {
58
59	class SurfaceDiffusion: public StaticAnalyser {
60
61	public:
62	SurfaceDiffusion(SimInfo* info, const std::string& filename, const std::string& sele, RealType len);
63	virtual ~SurfaceDiffusion();
64
65	virtual void process();
66
67	private:
68
69	double round(double r);
70	void solventAccessible();
71	void mobileAtomsFirst();
72	void mobileAtomsLast();
73	void mobileAtoms();
74	void positionCorrelation();
75
76	Snapshot* currentSnapshot_;
77
78	int nProcessed_;
79	std::string selectionScript_;
80	SelectionEvaluator evaluator_;
81	SelectionManager seleMan1_;
82
83	string filename_;
84	int bins_;
85	int selectionCount_;
86	double singleMoveDistance_;
87	int frames_;
88	bool doSolvent_;
89
90
91	//All positions of all frames of selected indices
92	//positions_[0][i]
93	// First particle at frame i
94	std::vector< std::vector<Vector3d> > positions_;
95	std::vector< std::vector<Vector3d> > positions2_;
96
97	//mobility of particle i at time j
98	// moBool[i][j]
99	// moBool.resize(selectionCount_);
100	// for(){
101	// moBool[i].resize(frames);
102	// }
103	std::vector< std::vector<bool> > moBool_;
104	std::vector< std::vector<bool> > moBool2_;
105
106	std::vector< std::vector<StuntDouble*> > gridSD_;
107	std::vector<StuntDouble*> gridHighZ_;
108	std::vector<StuntDouble*> gridLowZ_;
109	std::vector<StuntDouble*> forIndex_;
110	std::vector<Vector3d> firstPosition_;
111	std::vector<Vector3d> lastPosition_;
112
113
114	std::vector<int> SAIndices_;
115	std::vector<int> mobileIndices_;
116	std::vector<int> indices_;
117	std::vector<int> count_;
118
119	std::vector<RealType> xHist_;
120	std::vector<RealType> yHist_;
121	std::vector<RealType> rHist_;
122
123	RealType minDistance_;
124	RealType probe_;
125	};
126
127	}
128	#endif
129
130
131