OOPSE/libmdtools/Molecule.hpp

#ifndef _MOLECULE_H_
#define _MOLECULE_H_

#include "Atom.hpp"
#include "SRI.hpp"
#include "MoleculeStamp.hpp"
#include "RigidBody.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 nRigidBodies; // .. .. .. . rigid bodies ... .. 
  int nOriented; // .. . . . .. . oriented atoms . . . 

  Atom** myAtoms;      // the array of atoms
  Bond** myBonds;      // arrays of all the short range interactions
  Bend** myBends;
  Torsion** myTorsions;
  RigidBody** myRigidBodies;
} 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 getNRigidBodies( void ) {return nRigidBodies;}
  int getNOriented( void )    {return nOriented;}
  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;}
  RigidBody** getMyRigidBodies( void ) {return myRigidBodies;}
  
  void setStampID( int info ) {stampID = info;} 

  void calcForces( void );
  void atoms2rigidBodies( 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 nRigidBodies; // .. . . .. .rigid bodies . . .. . . 
  int nOriented; // .. . . . .. . oriented atoms . . . 
  int nMembers;  // .. . . . . . .atoms (legacy code) . . . 

  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;
  RigidBody** myRigidBodies;
  
};

#endif
Revision:	1097
Committed:	Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File size:	2836 byte(s)
Log Message:	Changes for RigidBody dynamics (Somewhat extensive)
#	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	1097	#include "RigidBody.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	gezelter	1097	int nRigidBodies; // .. .. .. . rigid bodies ... ..
17	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
18	gezelter	446
19	mmeineke	412	Atom** myAtoms; // the array of atoms
20	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
21			Bend** myBends;
22			Torsion** myTorsions;
23	gezelter	1097	RigidBody** myRigidBodies;
24	mmeineke	407	} molInit;
25
26	mmeineke	377	class Molecule{
27
28			public:
29
30	mmeineke	407	Molecule( void );
31			~Molecule( void );
32	mmeineke	377
33	mmeineke	407	void initialize( molInit &theInit );
34	chuckv	438
35			void setMyIndex( int theIndex ){ myIndex = theIndex;}
36	gezelter	490	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
37	mmeineke	489
38			int getMyIndex( void ) { return myIndex; }
39			int getGlobalIndex( void ) { return globalIndex; }
40	mmeineke	423
41	gezelter	1097	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 getNRigidBodies( void ) {return nRigidBodies;}
46			int getNOriented( void ) {return nOriented;}
47			int getNMembers ( void ) {return nMembers;}
48			int getStampID ( void ) {return stampID;}
49	mmeineke	407
50	gezelter	1097	Atom** getMyAtoms ( void ) {return myAtoms;}
51			Bond** getMyBonds ( void ) {return myBonds;}
52			Bend** getMyBends ( void ) {return myBends;}
53			Torsion** getMyTorsions( void ) {return myTorsions;}
54			RigidBody** getMyRigidBodies( void ) {return myRigidBodies;}
55	mmeineke	377
56	gezelter	1097	void setStampID( int info ) {stampID = info;}
57	mmeineke	423
58			void calcForces( void );
59	gezelter	1097	void atoms2rigidBodies( void );
60	mmeineke	423	double getPotential( void );
61	mmeineke	377
62	mmeineke	435	void printMe( void );
63	mmeineke	377
64	mmeineke	449	void getCOM( double COM[3] );
65	mmeineke	452	void moveCOM( double delta[3] );
66	gezelter	475	double getCOMvel( double COMvel[3] );
67	tim	658
68			double getTotalMass();
69	gezelter	446
70	mmeineke	377	private:
71
72	mmeineke	407	int stampID; // the ID in the BASS component stamp array
73			int nAtoms; // the number of atoms in the molecule
74			int nBonds; // ... .. .. . .bonds .. .. . . . .
75			int nBends; // . . . . .. . .bends . . . . .. .
76	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
77	gezelter	1097	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
78	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
79	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
80	mmeineke	407
81	gezelter	483	int myIndex; // mostly just for debug (and for making pressure calcs work)
82	mmeineke	489	int globalIndex;
83	chuckv	438
84	mmeineke	407	Atom** myAtoms; // the array of atoms
85	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
86	mmeineke	407	Bend** myBends;
87			Torsion** myTorsions;
88	gezelter	1097	RigidBody** myRigidBodies;
89	mmeineke	407
90	mmeineke	377	};
91
92			#endif