src/visitors/AtomData.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 VISITOR_ATOMDATA_HPP
#define VISITOR_ATOMDATA_HPP
#include <string>
#include <vector>

#include "utils/GenericData.hpp"
#include "math/Vector3.hpp"

namespace OpenMD {

  struct AtomInfo {
    AtomInfo() : hasCharge(false), hasVector(false), hasVelocity(false), 
                 hasForce(false), hasElectricField(false), 
                 pos(V3Zero), vec(V3Zero), vel(V3Zero), frc(V3Zero), 
                 charge(0.0), eField(V3Zero) {}
    
    std::string atomTypeName;
    Vector3d pos;
    Vector3d vec;  
    Vector3d vel;  
    Vector3d frc;  
    Vector3d eField;
    RealType charge;
    bool hasCharge;
    bool hasVector;
    bool hasVelocity;
    bool hasForce;
    bool hasElectricField;
  };

  class AtomData : public GenericData{
  public:

    AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {}

    ~AtomData() {
      std::vector<AtomInfo*>::iterator i;
      AtomInfo* atomInfo;

      for(atomInfo = beginAtomInfo(i); atomInfo; atomInfo  = nextAtomInfo(i)) {
        delete atomInfo;
      }
      data.clear();
    }
        
    void addAtomInfo(AtomInfo* info) {data.push_back(info);}

    void clearAllAtomInfo();

    AtomInfo* beginAtomInfo(std::vector<AtomInfo*>::iterator& i){
      i = data.begin();
      return i != data.end()? *i : NULL;
    }

    AtomInfo* nextAtomInfo(std::vector<AtomInfo*>::iterator& i){
      ++i;
      return i != data.end()? *i: NULL;
    }

    std::vector<AtomInfo*> getData() {return data;}

    int getSize() {return data.size();}

  protected:

    std::vector<AtomInfo*> data;
  };


}
#endif //VISITOR_ATOMDATA_HPP
Revision:	1871
Committed:	Fri May 10 14:59:13 2013 UTC (11 years, 11 months ago) by gezelter
File size:	3784 byte(s)
Log Message:	Bugs in the FQ samples, fixed for Dump2XYZ to print out charges and electric fields
#	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	#ifndef VISITOR_ATOMDATA_HPP
44	#define VISITOR_ATOMDATA_HPP
45	#include <string>
46	#include <vector>
47
48	#include "utils/GenericData.hpp"
49	#include "math/Vector3.hpp"
50
51	namespace OpenMD {
52
53	struct AtomInfo {
54	AtomInfo() : hasCharge(false), hasVector(false), hasVelocity(false),
55	hasForce(false), hasElectricField(false),
56	pos(V3Zero), vec(V3Zero), vel(V3Zero), frc(V3Zero),
57	charge(0.0), eField(V3Zero) {}
58
59	std::string atomTypeName;
60	Vector3d pos;
61	Vector3d vec;
62	Vector3d vel;
63	Vector3d frc;
64	Vector3d eField;
65	RealType charge;
66	bool hasCharge;
67	bool hasVector;
68	bool hasVelocity;
69	bool hasForce;
70	bool hasElectricField;
71	};
72
73	class AtomData : public GenericData{
74	public:
75
76	AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {}
77
78	~AtomData() {
79	std::vector<AtomInfo*>::iterator i;
80	AtomInfo* atomInfo;
81
82	for(atomInfo = beginAtomInfo(i); atomInfo; atomInfo = nextAtomInfo(i)) {
83	delete atomInfo;
84	}
85	data.clear();
86	}
87
88	void addAtomInfo(AtomInfo* info) {data.push_back(info);}
89
90	void clearAllAtomInfo();
91
92	AtomInfo* beginAtomInfo(std::vector<AtomInfo*>::iterator& i){
93	i = data.begin();
94	return i != data.end()? *i : NULL;
95	}
96
97	AtomInfo* nextAtomInfo(std::vector<AtomInfo*>::iterator& i){
98	++i;
99	return i != data.end()? *i: NULL;
100	}
101
102	std::vector<AtomInfo*> getData() {return data;}
103
104	int getSize() {return data.size();}
105
106	protected:
107
108	std::vector<AtomInfo*> data;
109	};
110
111
112	}
113	#endif //VISITOR_ATOMDATA_HPP