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"

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;}

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

  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:	1167
Committed:	Wed May 12 16:38:45 2004 UTC (20 years, 1 month ago) by tim
File size:	3556 byte(s)
Log Message:	get rid of rc and massratio from simState, creat cutoff group forevery atom which does not belong to cutoff group defined at mdl file
#	User	Rev	Content
1	mmeineke	377	#ifndef _MOLECULE_H_
2			#define _MOLECULE_H_
3
4	tim	1157	#include <set>
5			#include <vector>
6
7	mmeineke	377	#include "Atom.hpp"
8			#include "SRI.hpp"
9	mmeineke	407	#include "MoleculeStamp.hpp"
10	gezelter	1097	#include "RigidBody.hpp"
11	tim	1157	#include "CutoffGroup.hpp"
12	mmeineke	377
13	tim	1157	using namespace std;
14
15	mmeineke	407	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	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
22	gezelter	1097	int nRigidBodies; // .. .. .. . rigid bodies ... ..
23	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
24	tim	1157
25	mmeineke	412	Atom** myAtoms; // the array of atoms
26	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
27			Bend** myBends;
28			Torsion** myTorsions;
29	gezelter	1104	vector<RigidBody*> myRigidBodies;
30			vector<StuntDouble*> myIntegrableObjects;
31	tim	1157	vector<CutoffGroup*> myCutoffGroups;
32	mmeineke	407	} molInit;
33
34	mmeineke	377	class Molecule{
35
36			public:
37
38	mmeineke	407	Molecule( void );
39			~Molecule( void );
40	mmeineke	377
41	mmeineke	407	void initialize( molInit &theInit );
42	chuckv	438
43			void setMyIndex( int theIndex ){ myIndex = theIndex;}
44	tim	1108	int getMyIndex( void ) { return myIndex; }
45
46			int getGlobalIndex( void ) { return globalIndex; }
47	gezelter	490	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
48	mmeineke	489
49	gezelter	1097	int getNAtoms ( void ) {return nAtoms;}
50			int getNBonds ( void ) {return nBonds;}
51			int getNBends ( void ) {return nBends;}
52			int getNTorsions( void ) {return nTorsions;}
53	gezelter	1104	int getNRigidBodies( void ) {return myRigidBodies.size();}
54	gezelter	1097	int getNOriented( void ) {return nOriented;}
55			int getNMembers ( void ) {return nMembers;}
56			int getStampID ( void ) {return stampID;}
57	mmeineke	407
58	gezelter	1097	Atom** getMyAtoms ( void ) {return myAtoms;}
59			Bond** getMyBonds ( void ) {return myBonds;}
60			Bend** getMyBends ( void ) {return myBends;}
61			Torsion** getMyTorsions( void ) {return myTorsions;}
62	gezelter	1104	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
63	tim	1108	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
64	tim	1157
65			CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
66			i = myCutoffGroups.begin();
67			return i != myCutoffGroups.end()? *i : NULL;
68			}
69
70			CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
71			i++;
72			return i != myCutoffGroups.end()? *i : NULL;
73			}
74
75			int getNCutoffGroups() {return nCutoffGroups;}
76	mmeineke	377
77	gezelter	1097	void setStampID( int info ) {stampID = info;}
78	mmeineke	423
79			void calcForces( void );
80	gezelter	1097	void atoms2rigidBodies( void );
81	mmeineke	423	double getPotential( void );
82	mmeineke	377
83	mmeineke	435	void printMe( void );
84	mmeineke	377
85	mmeineke	449	void getCOM( double COM[3] );
86	mmeineke	452	void moveCOM( double delta[3] );
87	gezelter	475	double getCOMvel( double COMvel[3] );
88	tim	658
89			double getTotalMass();
90	gezelter	446
91	mmeineke	377	private:
92
93	mmeineke	407	int stampID; // the ID in the BASS component stamp array
94			int nAtoms; // the number of atoms in the molecule
95			int nBonds; // ... .. .. . .bonds .. .. . . . .
96			int nBends; // . . . . .. . .bends . . . . .. .
97	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
98	gezelter	1097	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
99	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
100	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
101	tim	1157	int nCutoffGroups;
102
103	gezelter	483	int myIndex; // mostly just for debug (and for making pressure calcs work)
104	mmeineke	489	int globalIndex;
105	chuckv	438
106	mmeineke	407	Atom** myAtoms; // the array of atoms
107	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
108	mmeineke	407	Bend** myBends;
109			Torsion** myTorsions;
110	gezelter	1104	vector<RigidBody*> myRigidBodies;
111			vector<StuntDouble*> myIntegrableObjects;
112	tim	1157	vector<CutoffGroup*> myCutoffGroups;
113	gezelter	1104
114	tim	1140
115	mmeineke	377	};
116
117			#endif