src/primitives/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"

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;
} 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;}

  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;
};

#endif
Revision:	2
Committed:	Fri Sep 24 04:16:43 2004 UTC (21 years, 1 month ago) by gezelter
File size:	3691 byte(s)
Log Message:	Import of OOPSE v. 2.0
#	User	Rev	Content
1	gezelter	2	#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
13			using namespace std;
14
15			typedef struct{
16
17			int stampID; // the ID in the BASS component stamp array
18			int nAtoms; // the number of atoms in the molecule
19			int nBonds; // ... .. .. . .bonds .. .. . . . .
20			int nBends; // . . . . .. . .bends . . . . .. .
21			int nTorsions; // .. . . .. . . torsions . . .. . .
22			int nRigidBodies; // .. .. .. . rigid bodies ... ..
23			int nOriented; // .. . . . .. . oriented atoms . . .
24
25			Atom** myAtoms; // the array of atoms
26			Bond** myBonds; // arrays of all the short range interactions
27			Bend** myBends;
28			Torsion** myTorsions;
29			vector<RigidBody*> myRigidBodies;
30			vector<StuntDouble*> myIntegrableObjects;
31			vector<CutoffGroup*> myCutoffGroups;
32			} molInit;
33
34			class Molecule{
35
36			public:
37
38			Molecule( void );
39			~Molecule( void );
40
41			void initialize( molInit &theInit );
42
43			void setMyIndex( int theIndex ){ myIndex = theIndex;}
44			int getMyIndex( void ) { return myIndex; }
45
46			int getGlobalIndex( void ) { return globalIndex; }
47			void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
48
49			int getNAtoms ( void ) {return nAtoms;}
50			int getNBonds ( void ) {return nBonds;}
51			int getNBends ( void ) {return nBends;}
52			int getNTorsions( void ) {return nTorsions;}
53			int getNRigidBodies( void ) {return myRigidBodies.size();}
54			int getNOriented( void ) {return nOriented;}
55			int getNMembers ( void ) {return nMembers;}
56			int getStampID ( void ) {return stampID;}
57
58			Atom** getMyAtoms ( void ) {return myAtoms;}
59			Bond** getMyBonds ( void ) {return myBonds;}
60			Bend** getMyBends ( void ) {return myBends;}
61			Torsion** getMyTorsions( void ) {return myTorsions;}
62			vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
63			vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
64
65			//beginCutoffGroup return the first group and initialize the iterator
66			CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
67			i = myCutoffGroups.begin();
68			return i != myCutoffGroups.end()? *i : NULL;
69			}
70
71			//nextCutoffGroup return next cutoff group based on the iterator
72			CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
73			i++;
74			return i != myCutoffGroups.end()? *i : NULL;
75			}
76
77			int getNCutoffGroups() {return nCutoffGroups;}
78
79			void setStampID( int info ) {stampID = info;}
80
81			void calcForces( void );
82			void atoms2rigidBodies( void );
83			double getPotential( void );
84
85			void printMe( void );
86
87			void getCOM( double COM[3] );
88			void moveCOM( double delta[3] );
89			double getCOMvel( double COMvel[3] );
90
91			double getTotalMass();
92
93			private:
94
95			int stampID; // the ID in the BASS component stamp array
96			int nAtoms; // the number of atoms in the molecule
97			int nBonds; // ... .. .. . .bonds .. .. . . . .
98			int nBends; // . . . . .. . .bends . . . . .. .
99			int nTorsions; // .. . . .. . . torsions . . .. . .
100			int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
101			int nOriented; // .. . . . .. . oriented atoms . . .
102			int nMembers; // .. . . . . . .atoms (legacy code) . . .
103			int nCutoffGroups;
104
105			int myIndex; // mostly just for debug (and for making pressure calcs work)
106			int globalIndex;
107
108			Atom** myAtoms; // the array of atoms
109			Bond** myBonds; // arrays of all the short range interactions
110			Bend** myBends;
111			Torsion** myTorsions;
112			vector<RigidBody*> myRigidBodies;
113			vector<StuntDouble*> myIntegrableObjects;
114			vector<CutoffGroup*> myCutoffGroups;
115			};
116
117			#endif