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 . . . 
  int nExcludes; // . . .. . . . .exclude pairs.. . . . 

  double* COM;   // the location of the center of mass of the molecule
  
  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 );

  void setMyIndex( int theIndex ){ myIndex = theIndex;}
 
  int getNAtoms   ( void ) {return nAtoms;}
  int getNBonds   ( void ) {return nBonds;}
  int getNBends   ( void ) {return nBends;}
  int getNTorsions( void ) {return nTorsions;}
  int getNOriented( void ) {return nOriented;}
  int getNExcludes( void ) {return nExcludes;}
  int getNMembers ( void ) {return nMembers;}
  int getStampID  ( void ) {return stampID;}

  Atom**     getMyAtoms   ( void ) {return myAtoms;}
  Bond**     getMyBonds   ( void ) {return myBonds;}
  Bend**     getMyBends   ( void ) {return myBends;}
  Torsion**  getMyTorsions( void ) {return myTorsions;}
  Exclude**  getMyExcludes( void ) {return myExcludes;}
  
  void setStampID( int info ) {stampID = info;}

  void calcForces( void );
  double getPotential( void );
  
  void printMe( void );

  double* getCOM();
  void moveCOM(double* delta);

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;  // .. . . . . . .atoms (legacy code) . . . 
  int nExcludes; // . . . . .. .. excludes .. . . 

  int myIndex; // mostly just for debug

  Atom** myAtoms;     // the array of atoms
  Bond** myBonds;     // arrays of all the short range interactions
  Bend** myBends;
  Torsion** myTorsions;
  Exclude** myExcludes; // array of the excluded pairs of long range forces
  
  double* COM;
};

#endif
Revision:	446
Committed:	Thu Apr 3 20:19:50 2003 UTC (21 years, 3 months ago) by gezelter
File size:	2602 byte(s)
Log Message:	Starting work on NPT
#	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	425	int nExcludes; // . . .. . . . .exclude pairs.. . . .
18	gezelter	446
19			double* COM; // the location of the center of mass of the molecule
20	mmeineke	407
21	mmeineke	412	Atom** myAtoms; // the array of atoms
22			Exclude** myExcludes;// the array of Excluded pairs
23	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
24			Bend** myBends;
25			Torsion** myTorsions;
26
27
28			} molInit;
29
30	mmeineke	377	class Molecule{
31
32			public:
33
34	mmeineke	407	Molecule( void );
35			~Molecule( void );
36	mmeineke	377
37	mmeineke	407	void initialize( molInit &theInit );
38	chuckv	438
39			void setMyIndex( int theIndex ){ myIndex = theIndex;}
40	mmeineke	423
41			int getNAtoms ( void ) {return nAtoms;}
42			int getNBonds ( void ) {return nBonds;}
43			int getNBends ( void ) {return nBends;}
44			int getNTorsions( void ) {return nTorsions;}
45			int getNOriented( void ) {return nOriented;}
46			int getNExcludes( void ) {return nExcludes;}
47			int getNMembers ( void ) {return nMembers;}
48			int getStampID ( void ) {return stampID;}
49	mmeineke	407
50	mmeineke	423	Atom** getMyAtoms ( void ) {return myAtoms;}
51			Bond** getMyBonds ( void ) {return myBonds;}
52			Bend** getMyBends ( void ) {return myBends;}
53	mmeineke	424	Torsion** getMyTorsions( void ) {return myTorsions;}
54			Exclude** getMyExcludes( void ) {return myExcludes;}
55	mmeineke	377
56	mmeineke	423	void setStampID( int info ) {stampID = info;}
57
58			void calcForces( void );
59			double getPotential( void );
60	mmeineke	377
61	mmeineke	435	void printMe( void );
62	mmeineke	377
63	gezelter	446	double* getCOM();
64			void moveCOM(double* delta);
65
66	mmeineke	377	private:
67
68	mmeineke	407	int stampID; // the ID in the BASS component stamp array
69			int nAtoms; // the number of atoms in the molecule
70			int nBonds; // ... .. .. . .bonds .. .. . . . .
71			int nBends; // . . . . .. . .bends . . . . .. .
72	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
73			int nOriented; // .. . . . .. . oriented atoms . . .
74	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
75			int nExcludes; // . . . . .. .. excludes .. . .
76	mmeineke	407
77	chuckv	438	int myIndex; // mostly just for debug
78
79	mmeineke	407	Atom** myAtoms; // the array of atoms
80	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
81	mmeineke	407	Bend** myBends;
82			Torsion** myTorsions;
83	mmeineke	423	Exclude** myExcludes; // array of the excluded pairs of long range forces
84	mmeineke	407
85	gezelter	446	double* COM;
86	mmeineke	377	};
87
88			#endif