OOPSE/libmdtools/Molecule.hpp

#ifndef _MOLECULE_H_
#define _MOLECULE_H_

#include "Atom.hpp"
#include "SRI.hpp"
#include "MoleculeStamp.hpp"
#include "Exclude.hpp"

typedef struct{
  
  int stampID;   // the ID in the BASS component stamp array
  int nAtoms;    // the number of atoms in the molecule
  int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
  int nBends;    // . . . . .. . .bends . . . . .. . 
  int nTorsions; // .. . . .. . . torsions . . .. . . 
  int nOriented; // .. . . . .. . oriented atoms . . . 
  
  Atom** myAtoms;      // the array of atoms
  Exclude** myExcludes;// the array of Excluded pairs 
  Bond** myBonds;      // arrays of all the short range interactions
  Bend** myBends;
  Torsion** myTorsions;


} molInit;

class Molecule{

public:
  
  Molecule( void );
  ~Molecule( void );

  void initialize( molInit &theInit );

  int   getNMembers( void )  { return nMembers; }
  int   getStartAtom( void ) { return startAtom; }
  int   getEndAtom( void )   { return endAtom; }
  int   getStampID( void )   { return stampID; }
  
  void   setStampID( int info )   { stampID = info; }
  

private:

  int stampID;   // the ID in the BASS component stamp array
  int nAtoms;    // the number of atoms in the molecule
  int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
  int nBends;    // . . . . .. . .bends . . . . .. . 
  int nTorsions; // .. . . .. . . torsions . . .. . . 
  int nOriented; // .. . . . .. . oriented atoms . . . 
  int nMembers;

  Atom** myAtoms;     // the array of atoms
  Bond** myBonds;      // arrays of all the short range interactions
  Bend** myBends;
  Torsion** myTorsions;
  
  int startAtom;
  int endAtom;


};

#endif
Revision:	422
Committed:	Thu Mar 27 19:21:42 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	1656 byte(s)
Log Message:	finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
#	Content
1	#ifndef _MOLECULE_H_
2	#define _MOLECULE_H_
3
4	#include "Atom.hpp"
5	#include "SRI.hpp"
6	#include "MoleculeStamp.hpp"
7	#include "Exclude.hpp"
8
9	typedef struct{
10
11	int stampID; // the ID in the BASS component stamp array
12	int nAtoms; // the number of atoms in the molecule
13	int nBonds; // ... .. .. . .bonds .. .. . . . .
14	int nBends; // . . . . .. . .bends . . . . .. .
15	int nTorsions; // .. . . .. . . torsions . . .. . .
16	int nOriented; // .. . . . .. . oriented atoms . . .
17
18	Atom** myAtoms; // the array of atoms
19	Exclude** myExcludes;// the array of Excluded pairs
20	Bond** myBonds; // arrays of all the short range interactions
21	Bend** myBends;
22	Torsion** myTorsions;
23
24
25	} molInit;
26
27	class Molecule{
28
29	public:
30
31	Molecule( void );
32	~Molecule( void );
33
34	void initialize( molInit &theInit );
35
36	int getNMembers( void ) { return nMembers; }
37	int getStartAtom( void ) { return startAtom; }
38	int getEndAtom( void ) { return endAtom; }
39	int getStampID( void ) { return stampID; }
40
41	void setStampID( int info ) { stampID = info; }
42
43
44	private:
45
46	int stampID; // the ID in the BASS component stamp array
47	int nAtoms; // the number of atoms in the molecule
48	int nBonds; // ... .. .. . .bonds .. .. . . . .
49	int nBends; // . . . . .. . .bends . . . . .. .
50	int nTorsions; // .. . . .. . . torsions . . .. . .
51	int nOriented; // .. . . . .. . oriented atoms . . .
52	int nMembers;
53
54	Atom** myAtoms; // the array of atoms
55	Bond** myBonds; // arrays of all the short range interactions
56	Bend** myBends;
57	Torsion** myTorsions;
58
59	int startAtom;
60	int endAtom;
61
62
63	};
64
65	#endif