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 (21 years, 4 months ago) by tim
File size:	3952 byte(s)
Log Message:	new rattle algorithm is working
#	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	tim	1234	#include "ConstraintPair.hpp"
13	mmeineke	377
14	tim	1157	using namespace std;
15
16	mmeineke	407	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	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
23	gezelter	1097	int nRigidBodies; // .. .. .. . rigid bodies ... ..
24	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
25	tim	1157
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	tim	1234	vector<ConstraintPair*> myConstraintPairs;
34	mmeineke	407	} molInit;
35
36	mmeineke	377	class Molecule{
37
38			public:
39
40	mmeineke	407	Molecule( void );
41			~Molecule( void );
42	mmeineke	377
43	mmeineke	407	void initialize( molInit &theInit );
44	chuckv	438
45			void setMyIndex( int theIndex ){ myIndex = theIndex;}
46	tim	1108	int getMyIndex( void ) { return myIndex; }
47
48			int getGlobalIndex( void ) { return globalIndex; }
49	gezelter	490	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
50	mmeineke	489
51	gezelter	1097	int getNAtoms ( void ) {return nAtoms;}
52			int getNBonds ( void ) {return nBonds;}
53			int getNBends ( void ) {return nBends;}
54			int getNTorsions( void ) {return nTorsions;}
55	gezelter	1104	int getNRigidBodies( void ) {return myRigidBodies.size();}
56	gezelter	1097	int getNOriented( void ) {return nOriented;}
57			int getNMembers ( void ) {return nMembers;}
58			int getStampID ( void ) {return stampID;}
59	mmeineke	407
60	gezelter	1097	Atom** getMyAtoms ( void ) {return myAtoms;}
61			Bond** getMyBonds ( void ) {return myBonds;}
62			Bend** getMyBends ( void ) {return myBends;}
63			Torsion** getMyTorsions( void ) {return myTorsions;}
64	gezelter	1104	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
65	tim	1108	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
66	tim	1157
67	tim	1234	//beginCutoffGroup return the first group and initialize the iterator
68	tim	1157	CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
69			i = myCutoffGroups.begin();
70			return i != myCutoffGroups.end()? *i : NULL;
71			}
72
73	tim	1234	//nextCutoffGroup return next cutoff group based on the iterator
74	tim	1157	CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
75			i++;
76			return i != myCutoffGroups.end()? *i : NULL;
77			}
78
79			int getNCutoffGroups() {return nCutoffGroups;}
80	tim	1234
81			int getNConstrains() {return myConstraintPairs.size();}
82			vector<ConstraintPair*>& getConstraintPairs() {return myConstraintPairs;}
83	mmeineke	377
84	tim	1234
85	gezelter	1097	void setStampID( int info ) {stampID = info;}
86	mmeineke	423
87			void calcForces( void );
88	gezelter	1097	void atoms2rigidBodies( void );
89	mmeineke	423	double getPotential( void );
90	mmeineke	377
91	mmeineke	435	void printMe( void );
92	mmeineke	377
93	mmeineke	449	void getCOM( double COM[3] );
94	mmeineke	452	void moveCOM( double delta[3] );
95	gezelter	475	double getCOMvel( double COMvel[3] );
96	tim	658
97			double getTotalMass();
98	gezelter	446
99	mmeineke	377	private:
100
101	mmeineke	407	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	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
106	gezelter	1097	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
107	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
108	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
109	tim	1157	int nCutoffGroups;
110
111	gezelter	483	int myIndex; // mostly just for debug (and for making pressure calcs work)
112	mmeineke	489	int globalIndex;
113	chuckv	438
114	mmeineke	407	Atom** myAtoms; // the array of atoms
115	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
116	mmeineke	407	Bend** myBends;
117			Torsion** myTorsions;
118	gezelter	1104	vector<RigidBody*> myRigidBodies;
119			vector<StuntDouble*> myIntegrableObjects;
120	tim	1157	vector<CutoffGroup*> myCutoffGroups;
121	tim	1234	vector<ConstraintPair*> myConstraintPairs;
122	gezelter	1104
123	mmeineke	377	};
124
125			#endif