OOPSE/libmdtools/Molecule.hpp

#ifndef _MOLECULE_H_
#define _MOLECULE_H_

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

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;
} 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;}
  
  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 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;

};

#endif
Revision:	1108
Committed:	Wed Apr 14 15:37:41 2004 UTC (20 years, 2 months ago) by tim
File size:	3035 byte(s)
Log Message:	Change DumpWriter and InitFromFile
#	User	Rev	Content
1	mmeineke	377	#ifndef _MOLECULE_H_
2			#define _MOLECULE_H_
3
4			#include "Atom.hpp"
5			#include "SRI.hpp"
6	mmeineke	407	#include "MoleculeStamp.hpp"
7	gezelter	1097	#include "RigidBody.hpp"
8	mmeineke	377
9	mmeineke	407	typedef struct{
10
11			int stampID; // the ID in the BASS component stamp array
12			int nAtoms; // the number of atoms in the molecule
13			int nBonds; // ... .. .. . .bonds .. .. . . . .
14			int nBends; // . . . . .. . .bends . . . . .. .
15	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
16	gezelter	1097	int nRigidBodies; // .. .. .. . rigid bodies ... ..
17	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
18	gezelter	446
19	mmeineke	412	Atom** myAtoms; // the array of atoms
20	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
21			Bend** myBends;
22			Torsion** myTorsions;
23	gezelter	1104	vector<RigidBody*> myRigidBodies;
24			vector<StuntDouble*> myIntegrableObjects;
25	mmeineke	407	} molInit;
26
27	mmeineke	377	class Molecule{
28
29			public:
30
31	mmeineke	407	Molecule( void );
32			~Molecule( void );
33	mmeineke	377
34	mmeineke	407	void initialize( molInit &theInit );
35	chuckv	438
36			void setMyIndex( int theIndex ){ myIndex = theIndex;}
37	tim	1108	int getMyIndex( void ) { return myIndex; }
38
39			int getGlobalIndex( void ) { return globalIndex; }
40	gezelter	490	void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
41	mmeineke	489
42	gezelter	1097	int getNAtoms ( void ) {return nAtoms;}
43			int getNBonds ( void ) {return nBonds;}
44			int getNBends ( void ) {return nBends;}
45			int getNTorsions( void ) {return nTorsions;}
46	gezelter	1104	int getNRigidBodies( void ) {return myRigidBodies.size();}
47	gezelter	1097	int getNOriented( void ) {return nOriented;}
48			int getNMembers ( void ) {return nMembers;}
49			int getStampID ( void ) {return stampID;}
50	mmeineke	407
51	gezelter	1097	Atom** getMyAtoms ( void ) {return myAtoms;}
52			Bond** getMyBonds ( void ) {return myBonds;}
53			Bend** getMyBends ( void ) {return myBends;}
54			Torsion** getMyTorsions( void ) {return myTorsions;}
55	gezelter	1104	vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
56	tim	1108	vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
57	mmeineke	377
58	gezelter	1097	void setStampID( int info ) {stampID = info;}
59	mmeineke	423
60			void calcForces( void );
61	gezelter	1097	void atoms2rigidBodies( void );
62	mmeineke	423	double getPotential( void );
63	mmeineke	377
64	mmeineke	435	void printMe( void );
65	mmeineke	377
66	mmeineke	449	void getCOM( double COM[3] );
67	mmeineke	452	void moveCOM( double delta[3] );
68	gezelter	475	double getCOMvel( double COMvel[3] );
69	tim	658
70			double getTotalMass();
71	gezelter	446
72	mmeineke	377	private:
73
74	mmeineke	407	int stampID; // the ID in the BASS component stamp array
75			int nAtoms; // the number of atoms in the molecule
76			int nBonds; // ... .. .. . .bonds .. .. . . . .
77			int nBends; // . . . . .. . .bends . . . . .. .
78	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
79	gezelter	1097	int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
80	gezelter	416	int nOriented; // .. . . . .. . oriented atoms . . .
81	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
82	mmeineke	407
83	gezelter	483	int myIndex; // mostly just for debug (and for making pressure calcs work)
84	mmeineke	489	int globalIndex;
85	chuckv	438
86	mmeineke	407	Atom** myAtoms; // the array of atoms
87	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
88	mmeineke	407	Bend** myBends;
89			Torsion** myTorsions;
90	gezelter	1104	vector<RigidBody*> myRigidBodies;
91			vector<StuntDouble*> myIntegrableObjects;
92
93	mmeineke	377	};
94
95			#endif