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 . . . 
  int nCutoffGroups;
  
  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;
  }

  bool belongToCutoffGroup(int index){
    return cutoffAtomSet.find(index) != cutoffAtomSet.end()? true: false;
  }

  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;
  set<int> cutoffAtomSet;  //global index of atoms belonging to cutoff group


};

#endif
Revision:	1157
Committed:	Tue May 11 20:33:41 2004 UTC (20 years, 2 months ago) by tim
File size:	3772 byte(s)
Log Message:	adding cutoffGroup into OOPSE
#	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	int nCutoffGroups;
25
26	mmeineke	412	Atom** myAtoms; // the array of atoms
27	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
28			Bend** myBends;
29			Torsion** myTorsions;
30	gezelter	1104	vector<RigidBody*> myRigidBodies;
31			vector<StuntDouble*> myIntegrableObjects;
32	tim	1157	vector<CutoffGroup*> myCutoffGroups;
33	mmeineke	407	} molInit;
34
35	mmeineke	377	class Molecule{
36
37			public:
38
39	mmeineke	407	Molecule( void );
40			~Molecule( void );
41	mmeineke	377
42	mmeineke	407	void initialize( molInit &theInit );
43	chuckv	438
44			void setMyIndex( int theIndex ){ myIndex = theIndex;}
45	tim	1108	int getMyIndex( void ) { return myIndex; }
46
47			int getGlobalIndex( void ) { return globalIndex; }
48	gezelter	490	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
49	mmeineke	489
50	gezelter	1097	int getNAtoms ( void ) {return nAtoms;}
51			int getNBonds ( void ) {return nBonds;}
52			int getNBends ( void ) {return nBends;}
53			int getNTorsions( void ) {return nTorsions;}
54	gezelter	1104	int getNRigidBodies( void ) {return myRigidBodies.size();}
55	gezelter	1097	int getNOriented( void ) {return nOriented;}
56			int getNMembers ( void ) {return nMembers;}
57			int getStampID ( void ) {return stampID;}
58	mmeineke	407
59	gezelter	1097	Atom** getMyAtoms ( void ) {return myAtoms;}
60			Bond** getMyBonds ( void ) {return myBonds;}
61			Bend** getMyBends ( void ) {return myBends;}
62			Torsion** getMyTorsions( void ) {return myTorsions;}
63	gezelter	1104	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
64	tim	1108	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
65	tim	1157
66			CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
67			i = myCutoffGroups.begin();
68			return i != myCutoffGroups.end()? *i : NULL;
69			}
70
71			CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
72			i++;
73			return i != myCutoffGroups.end()? *i : NULL;
74			}
75
76			bool belongToCutoffGroup(int index){
77			return cutoffAtomSet.find(index) != cutoffAtomSet.end()? true: false;
78			}
79
80			int getNCutoffGroups() {return nCutoffGroups;}
81	mmeineke	377
82	gezelter	1097	void setStampID( int info ) {stampID = info;}
83	mmeineke	423
84			void calcForces( void );
85	gezelter	1097	void atoms2rigidBodies( void );
86	mmeineke	423	double getPotential( void );
87	mmeineke	377
88	mmeineke	435	void printMe( void );
89	mmeineke	377
90	mmeineke	449	void getCOM( double COM[3] );
91	mmeineke	452	void moveCOM( double delta[3] );
92	gezelter	475	double getCOMvel( double COMvel[3] );
93	tim	658
94			double getTotalMass();
95	gezelter	446
96	mmeineke	377	private:
97
98	mmeineke	407	int stampID; // the ID in the BASS component stamp array
99			int nAtoms; // the number of atoms in the molecule
100			int nBonds; // ... .. .. . .bonds .. .. . . . .
101			int nBends; // . . . . .. . .bends . . . . .. .
102	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
103	gezelter	1097	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
104	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
105	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
106	tim	1157	int nCutoffGroups;
107
108	gezelter	483	int myIndex; // mostly just for debug (and for making pressure calcs work)
109	mmeineke	489	int globalIndex;
110	chuckv	438
111	mmeineke	407	Atom** myAtoms; // the array of atoms
112	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
113	mmeineke	407	Bend** myBends;
114			Torsion** myTorsions;
115	gezelter	1104	vector<RigidBody*> myRigidBodies;
116			vector<StuntDouble*> myIntegrableObjects;
117	tim	1157	vector<CutoffGroup*> myCutoffGroups;
118			set<int> cutoffAtomSet; //global index of atoms belonging to cutoff group
119	gezelter	1104
120	tim	1140
121	mmeineke	377	};
122
123			#endif