OOPSE/libmdtools/Molecule.hpp

#ifndef _MOLECULE_H_
#define _MOLECULE_H_

#include <set>
#include <vector>

#include "Atom.hpp"
#include "SRI.hpp"
#include "MoleculeStamp.hpp"
#include "RigidBody.hpp"
#include "CutoffGroup.hpp"
#include "ConstraintPair.hpp"

using namespace std;

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;
  vector<CutoffGroup*> myCutoffGroups;
  vector<ConstraintPair*> myConstraintPairs;
} molInit;

class Molecule{

public:
  
  Molecule( void );
  ~Molecule( void );

  void initialize( molInit &theInit );

  void setMyIndex( int theIndex ){ myIndex = theIndex;}
  int getMyIndex( void ) { return myIndex; }

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

  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;}
  vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}

  //beginCutoffGroup return the first group and initialize the iterator
  CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
    i = myCutoffGroups.begin();
    return i != myCutoffGroups.end()? *i : NULL;
  }

  //nextCutoffGroup return next cutoff group based on the iterator
  CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
    i++;
    return i != myCutoffGroups.end()? *i : NULL;
  }

  int getNCutoffGroups() {return nCutoffGroups;}

  int getNConstrains() {return myConstraintPairs.size();}
  vector<ConstraintPair*>& getConstraintPairs() {return myConstraintPairs;}
  
  
  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 nCutoffGroups;
  
  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;
  vector<CutoffGroup*> myCutoffGroups;
  vector<ConstraintPair*> myConstraintPairs;

};

#endif
Revision:	1234
Committed:	Fri Jun 4 03:15:31 2004 UTC (20 years ago) by tim
File size:	3952 byte(s)
Log Message:	new rattle algorithm is working
#	Content
1	#ifndef _MOLECULE_H_
2	#define _MOLECULE_H_
3
4	#include <set>
5	#include <vector>
6
7	#include "Atom.hpp"
8	#include "SRI.hpp"
9	#include "MoleculeStamp.hpp"
10	#include "RigidBody.hpp"
11	#include "CutoffGroup.hpp"
12	#include "ConstraintPair.hpp"
13
14	using namespace std;
15
16	typedef struct{
17
18	int stampID; // the ID in the BASS component stamp array
19	int nAtoms; // the number of atoms in the molecule
20	int nBonds; // ... .. .. . .bonds .. .. . . . .
21	int nBends; // . . . . .. . .bends . . . . .. .
22	int nTorsions; // .. . . .. . . torsions . . .. . .
23	int nRigidBodies; // .. .. .. . rigid bodies ... ..
24	int nOriented; // .. . . . .. . oriented atoms . . .
25
26	Atom** myAtoms; // the array of atoms
27	Bond** myBonds; // arrays of all the short range interactions
28	Bend** myBends;
29	Torsion** myTorsions;
30	vector<RigidBody*> myRigidBodies;
31	vector<StuntDouble*> myIntegrableObjects;
32	vector<CutoffGroup*> myCutoffGroups;
33	vector<ConstraintPair*> myConstraintPairs;
34	} molInit;
35
36	class Molecule{
37
38	public:
39
40	Molecule( void );
41	~Molecule( void );
42
43	void initialize( molInit &theInit );
44
45	void setMyIndex( int theIndex ){ myIndex = theIndex;}
46	int getMyIndex( void ) { return myIndex; }
47
48	int getGlobalIndex( void ) { return globalIndex; }
49	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
50
51	int getNAtoms ( void ) {return nAtoms;}
52	int getNBonds ( void ) {return nBonds;}
53	int getNBends ( void ) {return nBends;}
54	int getNTorsions( void ) {return nTorsions;}
55	int getNRigidBodies( void ) {return myRigidBodies.size();}
56	int getNOriented( void ) {return nOriented;}
57	int getNMembers ( void ) {return nMembers;}
58	int getStampID ( void ) {return stampID;}
59
60	Atom** getMyAtoms ( void ) {return myAtoms;}
61	Bond** getMyBonds ( void ) {return myBonds;}
62	Bend** getMyBends ( void ) {return myBends;}
63	Torsion** getMyTorsions( void ) {return myTorsions;}
64	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
65	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
66
67	//beginCutoffGroup return the first group and initialize the iterator
68	CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
69	i = myCutoffGroups.begin();
70	return i != myCutoffGroups.end()? *i : NULL;
71	}
72
73	//nextCutoffGroup return next cutoff group based on the iterator
74	CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
75	i++;
76	return i != myCutoffGroups.end()? *i : NULL;
77	}
78
79	int getNCutoffGroups() {return nCutoffGroups;}
80
81	int getNConstrains() {return myConstraintPairs.size();}
82	vector<ConstraintPair*>& getConstraintPairs() {return myConstraintPairs;}
83
84
85	void setStampID( int info ) {stampID = info;}
86
87	void calcForces( void );
88	void atoms2rigidBodies( void );
89	double getPotential( void );
90
91	void printMe( void );
92
93	void getCOM( double COM[3] );
94	void moveCOM( double delta[3] );
95	double getCOMvel( double COMvel[3] );
96
97	double getTotalMass();
98
99	private:
100
101	int stampID; // the ID in the BASS component stamp array
102	int nAtoms; // the number of atoms in the molecule
103	int nBonds; // ... .. .. . .bonds .. .. . . . .
104	int nBends; // . . . . .. . .bends . . . . .. .
105	int nTorsions; // .. . . .. . . torsions . . .. . .
106	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
107	int nOriented; // .. . . . .. . oriented atoms . . .
108	int nMembers; // .. . . . . . .atoms (legacy code) . . .
109	int nCutoffGroups;
110
111	int myIndex; // mostly just for debug (and for making pressure calcs work)
112	int globalIndex;
113
114	Atom** myAtoms; // the array of atoms
115	Bond** myBonds; // arrays of all the short range interactions
116	Bend** myBends;
117	Torsion** myTorsions;
118	vector<RigidBody*> myRigidBodies;
119	vector<StuntDouble*> myIntegrableObjects;
120	vector<CutoffGroup*> myCutoffGroups;
121	vector<ConstraintPair*> myConstraintPairs;
122
123	};
124
125	#endif