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 (12 years 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
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	246	*/
42
43	tim	132	#ifndef VISITOR_ATOMDATA_HPP
44			#define VISITOR_ATOMDATA_HPP
45	gezelter	246	#include <string>
46			#include <vector>
47
48	tim	132	#include "utils/GenericData.hpp"
49	gezelter	246	#include "math/Vector3.hpp"
50	tim	132
51	gezelter	1390	namespace OpenMD {
52	tim	132
53	gezelter	507	struct AtomInfo {
54	gezelter	1456	AtomInfo() : hasCharge(false), hasVector(false), hasVelocity(false),
55	gezelter	1871	hasForce(false), hasElectricField(false),
56			pos(V3Zero), vec(V3Zero), vel(V3Zero), frc(V3Zero),
57			charge(0.0), eField(V3Zero) {}
58	gezelter	1456
59	gezelter	407	std::string atomTypeName;
60	gezelter	246	Vector3d pos;
61	gezelter	1456	Vector3d vec;
62			Vector3d vel;
63			Vector3d frc;
64	gezelter	1871	Vector3d eField;
65	xsun	1219	RealType charge;
66			bool hasCharge;
67			bool hasVector;
68	gezelter	1456	bool hasVelocity;
69			bool hasForce;
70	gezelter	1871	bool hasElectricField;
71	gezelter	507	};
72	tim	132
73	gezelter	507	class AtomData : public GenericData{
74			public:
75	tim	132
76	gezelter	507	AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {}
77	tim	132
78	gezelter	507	~AtomData() {
79			std::vector<AtomInfo*>::iterator i;
80			AtomInfo* atomInfo;
81	gezelter	246
82	gezelter	507	for(atomInfo = beginAtomInfo(i); atomInfo; atomInfo = nextAtomInfo(i)) {
83			delete atomInfo;
84			}
85			data.clear();
86			}
87	gezelter	246
88	gezelter	507	void addAtomInfo(AtomInfo* info) {data.push_back(info);}
89	gezelter	246
90	gezelter	507	void clearAllAtomInfo();
91	gezelter	246
92	gezelter	507	AtomInfo* beginAtomInfo(std::vector<AtomInfo*>::iterator& i){
93			i = data.begin();
94			return i != data.end()? *i : NULL;
95			}
96	gezelter	246
97	gezelter	507	AtomInfo* nextAtomInfo(std::vector<AtomInfo*>::iterator& i){
98			++i;
99			return i != data.end()? *i: NULL;
100			}
101	gezelter	246
102	gezelter	507	std::vector<AtomInfo*> getData() {return data;}
103	gezelter	246
104	gezelter	507	int getSize() {return data.size();}
105	gezelter	246
106	gezelter	507	protected:
107	gezelter	246
108	gezelter	507	std::vector<AtomInfo*> data;
109			};
110	tim	132
111
112			}
113			#endif //VISITOR_ATOMDATA_HPP