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Comparing:
trunk/src/primitives/Atom.hpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/Atom.hpp (file contents), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

#	Line 1 | Line 1
1	<	#ifndef _ATOM_H_
2	<	#define _ATOM_H_
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	<	#include <string.h>
51	<	#include <stdlib.h>
6	<	#include <iostream>
50	>	#ifndef PRIMITIVES_ATOM_HPP
51	>	#define PRIMITIVES_ATOM_HPP
52
8	–	#include "brains/SimState.hpp"
53		#include "primitives/StuntDouble.hpp"
54	<	#include "visitors/BaseVisitor.hpp"
54	>	#include "types/AtomType.hpp"
55
56	<	class Atom : public StuntDouble {
57	<	public:
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	<	Atom(int theIndex, SimState* theConfig );
111	<	virtual ~Atom() {}
110	>	bool isShape()  {
111	>	return atomType_->isShape();
112	>	}
113	>
114	>	bool isMetal() {
115	>	return atomType_->isMetal();
116	>	}
117
118	<	virtual void setCoords(void);
118	>	bool isFluctuatingCharge() {
119	>	return atomType_->isFluctuatingCharge();
120	>	}
121
122	<	void getPos( double theP[3] );
123	<	void setPos( double theP[3] );
122	>	int getIdent() {
123	>	return atomType_->getIdent();
124	>	}
125	>
126	>	RealType getChargeMass() {
127	>	return chargeMass_;
128	>	}
129
130	<	void getVel( double theV[3] );
131	<	void setVel( double theV[3] );
130	>	void setChargeMass(RealType cm) {
131	>	chargeMass_ = cm;
132	>	}
133
134	<	void getFrc( double theF[3] );
135	<	void addFrc( double theF[3] );
136	<
137	<	virtual void zeroForces();
30	<
31	<	double getMass() {return c_mass;}
32	<	void setMass(double mass) {c_mass = mass;}
134	>	protected:
135	>	AtomType* atomType_;
136	>	RealType chargeMass_;
137	>	};
138
139	<	int getIndex() const {return index;}
35	<	void setIndex(int theIndex);
139	>	}//namespace OpenMD
140
141	<	char *getType() {return c_name;}
38	<	void setType(char * name) {strcpy(c_name,name);}
39	<
40	<	int getIdent( void ) { return ident; }
41	<	void setIdent( int info ) { ident = info; }
42	<
43	<	#ifdef IS_MPI
44	<	int getGlobalIndex( void ) { return myGlobalIndex; }
45	<	void setGlobalIndex( int info ) { myGlobalIndex = info; }
46	<	#endif // is_mpi
47	<
48	<	void setHasDipole( int value ) { has_dipole = value; }
49	<	int hasDipole( void ) { return has_dipole; }
50	<
51	<	void setHasCharge(int value) {has_charge = value;}
52	<	int hasCharge(void) {return has_charge;}
53	<
54	<
55	<	virtual void accept(BaseVisitor* v) {v->visit(this);}
56	<
57	<	protected:
58	<
59	<	SimState* myConfig;
60	<
61	<	double* pos; // the position array
62	<	double* vel; // the velocity array
63	<	double* frc; // the forc array
64	<	double* trq; // the torque vector  ( space fixed )
65	<	double* Amat; // the rotation matrix
66	<	double* mu;   // the array of dipole moments
67	<	double* ul;   // the lab frame unit directional vector
68	<
69	<	double zAngle; // the rotation about the z-axis ( body-fixed )
70	<
71	<	double c_mass; /* the mass of the atom in amu */
72	<
73	<	int index; /* set the atom's index */
74	<	int offset; // the atom's offset in the storage array
75	<	int offsetX, offsetY, offsetZ;
76	<
77	<	int Axx, Axy, Axz; // the rotational matrix indices
78	<	int Ayx, Ayy, Ayz;
79	<	int Azx, Azy, Azz;
80	<
81	<	char c_name[100]; /* it's name */
82	<	int ident;  // it's unique numeric identity.
83	<
84	<	int has_dipole; // dipole boolean
85	<	int has_charge; // charge boolean
86	<
87	<	bool hasCoords;
88	<
89	<	#ifdef IS_MPI
90	<	int myGlobalIndex;
91	<	#endif
92	<
93	<	};
94	<
95	<	#endif
141	>	#endif //PRIMITIVES_ATOM_HPP

Comparing:
trunk/src/primitives/Atom.hpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/Atom.hpp (property svn:keywords), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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