applications/staticProps/pAngle.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]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).                     
 *
 */
#ifndef APPLICATIONS_STATICPROPS_PANGLE_HPP
#define APPLICATIONS_STATICPROPS_PANGLE_HPP

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

using namespace std;
namespace OpenMD {
  
  class pAngle : public StaticAnalyser {
    
  public:
    pAngle(SimInfo* info, const string& filename, 
           const string& sele1, int nzbins);
    pAngle(SimInfo* info, const string& filename, 
           const string& sele1, const string& sele2, int nzbins);
    pAngle(SimInfo* info, const string& filename, 
           const string& sele, const int seleOffset, int nzbins);
    
    int getNThetaBins() {
      return nThetaBins_; 
    }
    
    virtual void process();
    
  private:
    
    void processHistogram();
    void writeProbs();
        
    Snapshot* currentSnapshot_;

    bool doVect_;
    bool doOffset_;
    string selectionScript1_;
    string selectionScript2_;
    SelectionManager seleMan1_;
    SelectionManager seleMan2_;       
    SelectionEvaluator evaluator1_;
    SelectionEvaluator evaluator2_;
    int seleOffset_;

    int nProcessed_;    
    int nThetaBins_;     
    vector<int> count_;
    vector<RealType> histogram_;
  };
  
}
#endif


Revision:	1979
Committed:	Sat Apr 5 20:56:01 2014 UTC (11 years, 1 month ago) by gezelter
File size:	3480 byte(s)
Log Message:	* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals * Added the ability to specify non-bonded constraints in a molecule * Added the ability to do selection offsets in the pAngle staticProps module
#	User	Rev	Content
1	gezelter	1413	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40	gezelter	1413	*
41			*/
42			#ifndef APPLICATIONS_STATICPROPS_PANGLE_HPP
43			#define APPLICATIONS_STATICPROPS_PANGLE_HPP
44
45			#include <string>
46			#include <vector>
47			#include "selection/SelectionEvaluator.hpp"
48			#include "selection/SelectionManager.hpp"
49			#include "utils/NumericConstant.hpp"
50			#include "applications/staticProps/StaticAnalyser.hpp"
51
52	gezelter	1979	using namespace std;
53	gezelter	1413	namespace OpenMD {
54
55			class pAngle : public StaticAnalyser {
56
57			public:
58	gezelter	1979	pAngle(SimInfo* info, const string& filename,
59			const string& sele1, int nzbins);
60			pAngle(SimInfo* info, const string& filename,
61			const string& sele1, const string& sele2, int nzbins);
62			pAngle(SimInfo* info, const string& filename,
63			const string& sele, const int seleOffset, int nzbins);
64	gezelter	1413
65			int getNThetaBins() {
66			return nThetaBins_;
67			}
68
69			virtual void process();
70
71			private:
72
73			void processHistogram();
74			void writeProbs();
75
76			Snapshot* currentSnapshot_;
77	gezelter	1979
78			bool doVect_;
79			bool doOffset_;
80			string selectionScript1_;
81			string selectionScript2_;
82			SelectionManager seleMan1_;
83			SelectionManager seleMan2_;
84			SelectionEvaluator evaluator1_;
85			SelectionEvaluator evaluator2_;
86			int seleOffset_;
87
88			int nProcessed_;
89			int nThetaBins_;
90			vector<int> count_;
91			vector<RealType> histogram_;
92	gezelter	1413	};
93
94			}
95			#endif
96
97
98