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
#	User	Rev	Content
1	mmeineke	377	#ifndef _MOLECULE_H_
2			#define _MOLECULE_H_
3
4			#include "Atom.hpp"
5			#include "SRI.hpp"
6	mmeineke	407	#include "MoleculeStamp.hpp"
7	gezelter	416	#include "Exclude.hpp"
8	mmeineke	377
9	mmeineke	407	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	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
16			int nOriented; // .. . . . .. . oriented atoms . . .
17	mmeineke	407
18	mmeineke	412	Atom** myAtoms; // the array of atoms
19			Exclude** myExcludes;// the array of Excluded pairs
20	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
21			Bend** myBends;
22			Torsion** myTorsions;
23
24
25			} molInit;
26
27	mmeineke	377	class Molecule{
28
29			public:
30
31	mmeineke	407	Molecule( void );
32			~Molecule( void );
33	mmeineke	377
34	mmeineke	407	void initialize( molInit &theInit );
35
36	mmeineke	377	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	mmeineke	407	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	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
51			int nOriented; // .. . . . .. . oriented atoms . . .
52			int nMembers;
53	mmeineke	407
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	mmeineke	377	int startAtom;
60			int endAtom;
61
62	mmeineke	407
63	mmeineke	377	};
64
65			#endif