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;}
  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }

  int getMyIndex( void ) { return myIndex; }
  int getGlobalIndex( void ) { return globalIndex; }
 
  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] );
  double getCOMvel( double COMvel[3] );
  
  double getTotalMass();

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 (and for making pressure calcs work)
  int globalIndex;

  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:	658
Committed:	Thu Jul 31 15:35:07 2003 UTC (20 years, 11 months ago) by tim
File size:	2823 byte(s)
Log Message:	Added Z constraint.
#	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	gezelter	490	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
39	mmeineke	489
40			int getMyIndex( void ) { return myIndex; }
41			int getGlobalIndex( void ) { return globalIndex; }
42	mmeineke	423
43			int getNAtoms ( void ) {return nAtoms;}
44			int getNBonds ( void ) {return nBonds;}
45			int getNBends ( void ) {return nBends;}
46			int getNTorsions( void ) {return nTorsions;}
47			int getNOriented( void ) {return nOriented;}
48			int getNExcludes( void ) {return nExcludes;}
49			int getNMembers ( void ) {return nMembers;}
50			int getStampID ( void ) {return stampID;}
51	mmeineke	407
52	mmeineke	423	Atom** getMyAtoms ( void ) {return myAtoms;}
53			Bond** getMyBonds ( void ) {return myBonds;}
54			Bend** getMyBends ( void ) {return myBends;}
55	mmeineke	424	Torsion** getMyTorsions( void ) {return myTorsions;}
56			Exclude** getMyExcludes( void ) {return myExcludes;}
57	mmeineke	377
58	mmeineke	423	void setStampID( int info ) {stampID = info;}
59	mmeineke	489
60	mmeineke	423
61	mmeineke	489
62
63	mmeineke	423	void calcForces( void );
64			double getPotential( void );
65	mmeineke	377
66	mmeineke	435	void printMe( void );
67	mmeineke	377
68	mmeineke	449	void getCOM( double COM[3] );
69	mmeineke	452	void moveCOM( double delta[3] );
70	gezelter	475	double getCOMvel( double COMvel[3] );
71	tim	658
72			double getTotalMass();
73	gezelter	446
74	mmeineke	377	private:
75
76	mmeineke	407	int stampID; // the ID in the BASS component stamp array
77			int nAtoms; // the number of atoms in the molecule
78			int nBonds; // ... .. .. . .bonds .. .. . . . .
79			int nBends; // . . . . .. . .bends . . . . .. .
80	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
81			int nOriented; // .. . . . .. . oriented atoms . . .
82	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
83			int nExcludes; // . . . . .. .. excludes .. . .
84	mmeineke	407
85	gezelter	483	int myIndex; // mostly just for debug (and for making pressure calcs work)
86	mmeineke	489	int globalIndex;
87	chuckv	438
88	mmeineke	407	Atom** myAtoms; // the array of atoms
89	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
90	mmeineke	407	Bend** myBends;
91			Torsion** myTorsions;
92	mmeineke	423	Exclude** myExcludes; // array of the excluded pairs of long range forces
93	mmeineke	407
94	mmeineke	377	};
95
96			#endif