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;
  vector<RigidBody*>   myRigidBodies;
  vector<StuntDouble*> myIntegrableObjects;
} 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 myRigidBodies.size();}
  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;}
  vector<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;
  vector<RigidBody*>   myRigidBodies;
  vector<StuntDouble*> myIntegrableObjects;

};

#endif
Revision:	1104
Committed:	Tue Apr 13 16:26:03 2004 UTC (20 years, 2 months ago) by gezelter
File size:	2955 byte(s)
Log Message:	Now molecules can keep track of their own IntegrableObjects (and RigidBodies). Also a bug-fix so that SimInfo can keep track of RigidBodies (which was done incorrectly before).
#	Content
1	#ifndef _MOLECULE_H_
2	#define _MOLECULE_H_
3
4	#include "Atom.hpp"
5	#include "SRI.hpp"
6	#include "MoleculeStamp.hpp"
7	#include "RigidBody.hpp"
8
9	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	int nTorsions; // .. . . .. . . torsions . . .. . .
16	int nRigidBodies; // .. .. .. . rigid bodies ... ..
17	int nOriented; // .. . . . .. . oriented atoms . . .
18
19	Atom** myAtoms; // the array of atoms
20	Bond** myBonds; // arrays of all the short range interactions
21	Bend** myBends;
22	Torsion** myTorsions;
23	vector<RigidBody*> myRigidBodies;
24	vector<StuntDouble*> myIntegrableObjects;
25	} molInit;
26
27	class Molecule{
28
29	public:
30
31	Molecule( void );
32	~Molecule( void );
33
34	void initialize( molInit &theInit );
35
36	void setMyIndex( int theIndex ){ myIndex = theIndex;}
37	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
38
39	int getMyIndex( void ) { return myIndex; }
40	int getGlobalIndex( void ) { return globalIndex; }
41
42	int getNAtoms ( void ) {return nAtoms;}
43	int getNBonds ( void ) {return nBonds;}
44	int getNBends ( void ) {return nBends;}
45	int getNTorsions( void ) {return nTorsions;}
46	int getNRigidBodies( void ) {return myRigidBodies.size();}
47	int getNOriented( void ) {return nOriented;}
48	int getNMembers ( void ) {return nMembers;}
49	int getStampID ( void ) {return stampID;}
50
51	Atom** getMyAtoms ( void ) {return myAtoms;}
52	Bond** getMyBonds ( void ) {return myBonds;}
53	Bend** getMyBends ( void ) {return myBends;}
54	Torsion** getMyTorsions( void ) {return myTorsions;}
55	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
56
57	void setStampID( int info ) {stampID = info;}
58
59	void calcForces( void );
60	void atoms2rigidBodies( void );
61	double getPotential( void );
62
63	void printMe( void );
64
65	void getCOM( double COM[3] );
66	void moveCOM( double delta[3] );
67	double getCOMvel( double COMvel[3] );
68
69	double getTotalMass();
70
71	private:
72
73	int stampID; // the ID in the BASS component stamp array
74	int nAtoms; // the number of atoms in the molecule
75	int nBonds; // ... .. .. . .bonds .. .. . . . .
76	int nBends; // . . . . .. . .bends . . . . .. .
77	int nTorsions; // .. . . .. . . torsions . . .. . .
78	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
79	int nOriented; // .. . . . .. . oriented atoms . . .
80	int nMembers; // .. . . . . . .atoms (legacy code) . . .
81
82	int myIndex; // mostly just for debug (and for making pressure calcs work)
83	int globalIndex;
84
85	Atom** myAtoms; // the array of atoms
86	Bond** myBonds; // arrays of all the short range interactions
87	Bend** myBends;
88	Torsion** myTorsions;
89	vector<RigidBody*> myRigidBodies;
90	vector<StuntDouble*> myIntegrableObjects;
91
92	};
93
94	#endif