src/primitives/Atom.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).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file Atom.hpp
 * @author    tlin
 * @date  10/22/2004
 * @version 1.0
 */ 

#ifndef PRIMITIVES_ATOM_HPP
#define PRIMITIVES_ATOM_HPP

#include "primitives/StuntDouble.hpp"
#include "types/AtomType.hpp"

namespace OpenMD{
  class Atom : public StuntDouble {
  public:
    Atom(AtomType* at);
    
    virtual std::string getType() {return atomType_->getName();}
    
    /**
     * Returns the inertia tensor of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     */ 
    virtual Mat3x3d getI();
    
    /**
     * Returns the gradient of this stuntdouble
     * @return the inertia tensor of this stuntdouble
     */ 
    virtual std::vector<RealType> getGrad();
    
    virtual void accept(BaseVisitor* v);
    
    /** 
     * Returns the AtomType of this Atom.
     * @return the atom type of this atom
     */
    AtomType* getAtomType() {
      return atomType_;
    }
    
    //forward  functions of AtomType class
    bool isCharge()  {
      return atomType_->isCharge(); 
    }
    
    bool isDirectional() {
      return atomType_->isDirectional(); 
    }
    
    bool isDipole()  { 
      return atomType_->isDipole(); 
    }
    
    bool isMultipole()  { 
      return atomType_->isMultipole(); 
    }
    
    bool isGayBerne()  {
      return atomType_->isGayBerne(); 
    }
            
    bool isSticky()  { 
      return atomType_->isSticky(); 
    }

    bool isShape()  { 
      return atomType_->isShape(); 
    }            
    
    bool isMetal() {
      return atomType_->isMetal();
    }

    int getIdent() {
      return atomType_->getIdent();
    }
    
  protected:
    AtomType* atomType_;
  };
  
}//namespace OpenMD

#endif //PRIMITIVES_ATOM_HPP
Revision:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	3899 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file Atom.hpp
45	* @author tlin
46	* @date 10/22/2004
47	* @version 1.0
48	*/
49
50	#ifndef PRIMITIVES_ATOM_HPP
51	#define PRIMITIVES_ATOM_HPP
52
53	#include "primitives/StuntDouble.hpp"
54	#include "types/AtomType.hpp"
55
56	namespace OpenMD{
57	class Atom : public StuntDouble {
58	public:
59	Atom(AtomType* at);
60
61	virtual std::string getType() {return atomType_->getName();}
62
63	/**
64	* Returns the inertia tensor of this stuntdouble
65	* @return the inertia tensor of this stuntdouble
66	*/
67	virtual Mat3x3d getI();
68
69	/**
70	* Returns the gradient of this stuntdouble
71	* @return the inertia tensor of this stuntdouble
72	*/
73	virtual std::vector<RealType> getGrad();
74
75	virtual void accept(BaseVisitor* v);
76
77	/**
78	* Returns the AtomType of this Atom.
79	* @return the atom type of this atom
80	*/
81	AtomType* getAtomType() {
82	return atomType_;
83	}
84
85	//forward functions of AtomType class
86	bool isCharge() {
87	return atomType_->isCharge();
88	}
89
90	bool isDirectional() {
91	return atomType_->isDirectional();
92	}
93
94	bool isDipole() {
95	return atomType_->isDipole();
96	}
97
98	bool isMultipole() {
99	return atomType_->isMultipole();
100	}
101
102	bool isGayBerne() {
103	return atomType_->isGayBerne();
104	}
105
106	bool isSticky() {
107	return atomType_->isSticky();
108	}
109
110	bool isShape() {
111	return atomType_->isShape();
112	}
113
114	bool isMetal() {
115	return atomType_->isMetal();
116	}
117
118	int getIdent() {
119	return atomType_->getIdent();
120	}
121
122	protected:
123	AtomType* atomType_;
124	};
125
126	}//namespace OpenMD
127
128	#endif //PRIMITIVES_ATOM_HPP