trunk/SHAPES/RigidBody.hpp

#ifndef __RIGIDBODY_HPP__
#define __RIGIDBODY_HPP__

#include <vector>
using namespace std;

class VDWAtom;

typedef struct {
  double vec[3];
  double& operator[](int index) {return vec[index];}  
} vec3;

typedef struct {
  double mat[3][3];
  double* operator[](int index) {return mat[index];}  
} mat3x3;

class RigidBody {

public:
  
  RigidBody();
  virtual ~RigidBody();
 
  void addAtom(VDWAtom* at);

  void getPos( double theP[3] );
  void setPos( double theP[3] );

  virtual bool isLinear() {return is_linear;}
  virtual int linearAxis() {return linear_axis;}

  double getMass( void ) { return mass; }

  void setEuler( double phi, double theta, double psi );
  void getQ( double the_q[4] ); // get the quanternions
  void setQ( double the_q[4] );

  void getA( double the_A[3][3] ); // get the full rotation matrix
  void setA( double the_A[3][3] );

  void getI( double the_I[3][3] );
  void lab2Body( double r[3] );
  void body2Lab( double r[3] );

  void calcRefCoords( void );
  void doEulerToRotMat(double euler[3], double myA[3][3] );
  void updateAtoms( void );

  void getGrad(double gradient[6] );
  void getEulerAngles( double myEuler[3] ); 
 
  double max(double x, double y);
  double min(double x, double y);
  
  double findMaxExtent( void );

  // utility routines

  void findCOM( void );

  vector<VDWAtom*> getAtoms() { return myAtoms;}
  int getNumAtoms() {return myAtoms.size();}

  void getAtomPos(double theP[3], int index);
  void getAtomRefCoor(double pos[3], int index);
  double getAtomRpar(int index);
  double getAtomEps(int index);
  char *getAtomType(int index);
  
protected:

  double mass;     // the total mass
  double pos[3];   // the position array (center of mass)
  double A[3][3];  // the rotation matrix 
  double I[3][3];  // the inertial tensor (body fixed)
  double sU[3][3]; // the standard unit vectors (body fixed)

  bool is_linear;
  int linear_axis;
  double momIntTol;

  vector<VDWAtom*> myAtoms;  // the vector of atoms
  vector<vec3> refCoords;
  vector<mat3x3> refOrients;

  char rbName[100]; //it will eventually be converted into string
};

#endif
Revision:	1286
Committed:	Tue Jun 22 20:38:04 2004 UTC (21 years, 4 months ago) by chrisfen
File size:	2121 byte(s)
Log Message:	Now prints out a .xyz file of the reference configuration
#	User	Rev	Content
1	gezelter	1271	#ifndef __RIGIDBODY_HPP__
2			#define __RIGIDBODY_HPP__
3
4			#include <vector>
5			using namespace std;
6
7			class VDWAtom;
8
9			typedef struct {
10			double vec[3];
11			double& operator[](int index) {return vec[index];}
12			} vec3;
13
14			typedef struct {
15			double mat[3][3];
16			double* operator[](int index) {return mat[index];}
17			} mat3x3;
18
19			class RigidBody {
20
21			public:
22
23			RigidBody();
24			virtual ~RigidBody();
25
26			void addAtom(VDWAtom* at);
27
28			void getPos( double theP[3] );
29			void setPos( double theP[3] );
30
31			virtual bool isLinear() {return is_linear;}
32			virtual int linearAxis() {return linear_axis;}
33
34			double getMass( void ) { return mass; }
35
36			void setEuler( double phi, double theta, double psi );
37			void getQ( double the_q[4] ); // get the quanternions
38			void setQ( double the_q[4] );
39
40			void getA( double the_A[3][3] ); // get the full rotation matrix
41			void setA( double the_A[3][3] );
42
43			void getI( double the_I[3][3] );
44			void lab2Body( double r[3] );
45			void body2Lab( double r[3] );
46
47			void calcRefCoords( void );
48	chrisfen	1276	void doEulerToRotMat(double euler[3], double myA[3][3] );
49	gezelter	1271	void updateAtoms( void );
50
51			void getGrad(double gradient[6] );
52			void getEulerAngles( double myEuler[3] );
53
54			double max(double x, double y);
55			double min(double x, double y);
56	chrisfen	1276
57			double findMaxExtent( void );
58	gezelter	1271
59			// utility routines
60
61			void findCOM( void );
62
63			vector<VDWAtom*> getAtoms() { return myAtoms;}
64			int getNumAtoms() {return myAtoms.size();}
65
66			void getAtomPos(double theP[3], int index);
67			void getAtomRefCoor(double pos[3], int index);
68	chrisfen	1281	double getAtomRpar(int index);
69			double getAtomEps(int index);
70	chrisfen	1286	char *getAtomType(int index);
71	chrisfen	1281
72	gezelter	1271	protected:
73
74			double mass; // the total mass
75			double pos[3]; // the position array (center of mass)
76			double A[3][3]; // the rotation matrix
77			double I[3][3]; // the inertial tensor (body fixed)
78			double sU[3][3]; // the standard unit vectors (body fixed)
79
80			bool is_linear;
81			int linear_axis;
82			double momIntTol;
83
84			vector<VDWAtom*> myAtoms; // the vector of atoms
85			vector<vec3> refCoords;
86			vector<mat3x3> refOrients;
87
88			char rbName[100]; //it will eventually be converted into string
89			};
90
91			#endif