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.. . . . 

  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 );

  void getCOM( double COM[3] );
  void moveCOM(double delta[3]);

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
  
};

#endif
Revision:	449
Committed:	Thu Apr 3 20:57:56 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	2527 byte(s)
Log Message:	a few fixes to simError.h also some fixes to Molecule.hpp
#	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	mmeineke	412	Atom** myAtoms; // the array of atoms
20			Exclude** myExcludes;// the array of Excluded pairs
21	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
22			Bend** myBends;
23			Torsion** myTorsions;
24
25
26			} molInit;
27
28	mmeineke	377	class Molecule{
29
30			public:
31
32	mmeineke	407	Molecule( void );
33			~Molecule( void );
34	mmeineke	377
35	mmeineke	407	void initialize( molInit &theInit );
36	chuckv	438
37			void setMyIndex( int theIndex ){ myIndex = theIndex;}
38	mmeineke	423
39			int getNAtoms ( void ) {return nAtoms;}
40			int getNBonds ( void ) {return nBonds;}
41			int getNBends ( void ) {return nBends;}
42			int getNTorsions( void ) {return nTorsions;}
43			int getNOriented( void ) {return nOriented;}
44			int getNExcludes( void ) {return nExcludes;}
45			int getNMembers ( void ) {return nMembers;}
46			int getStampID ( void ) {return stampID;}
47	mmeineke	407
48	mmeineke	423	Atom** getMyAtoms ( void ) {return myAtoms;}
49			Bond** getMyBonds ( void ) {return myBonds;}
50			Bend** getMyBends ( void ) {return myBends;}
51	mmeineke	424	Torsion** getMyTorsions( void ) {return myTorsions;}
52			Exclude** getMyExcludes( void ) {return myExcludes;}
53	mmeineke	377
54	mmeineke	423	void setStampID( int info ) {stampID = info;}
55
56			void calcForces( void );
57			double getPotential( void );
58	mmeineke	377
59	mmeineke	435	void printMe( void );
60	mmeineke	377
61	mmeineke	449	void getCOM( double COM[3] );
62			void moveCOM(double delta[3]);
63	gezelter	446
64	mmeineke	377	private:
65
66	mmeineke	407	int stampID; // the ID in the BASS component stamp array
67			int nAtoms; // the number of atoms in the molecule
68			int nBonds; // ... .. .. . .bonds .. .. . . . .
69			int nBends; // . . . . .. . .bends . . . . .. .
70	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
71			int nOriented; // .. . . . .. . oriented atoms . . .
72	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
73			int nExcludes; // . . . . .. .. excludes .. . .
74	mmeineke	407
75	chuckv	438	int myIndex; // mostly just for debug
76
77	mmeineke	407	Atom** myAtoms; // the array of atoms
78	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
79	mmeineke	407	Bend** myBends;
80			Torsion** myTorsions;
81	mmeineke	423	Exclude** myExcludes; // array of the excluded pairs of long range forces
82	mmeineke	407
83	mmeineke	377	};
84
85			#endif