mdtools/headers/LRI.hpp

#ifndef _LRI_H_
#define _LRI_H_

#include <stdio.h>
#include <fstream>

#include "Atom.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"

using namespace std;

class AllLong : public LRI{

public:
  AllLong( SimInfo* entry_plug );
  ~AllLong();
  void calc_forces();
  double get_potential() {return potentialE;}

private:
  
  int nPairs; // the number of excluded pairs
  int* pairI; // the array of excluded pairs
  int* pairJ;
  unsigned short int exclude; // boolean on whether there are any excludes

  int nAtoms;   // the number of atoms
  Atom** atoms; // the array of atom objects
  
  double boxX; // periodic boundry conditions
  double boxY;
  double boxZ;
  
  int nDipoles; // the number of dipoles in the system

  double rRF;        // the reaction field cut off radius
  double rTaper;     // the taper radius of the reaction field
  double dielectric; // the dielectric constant for the reaction field medium
   
  double* Rx; // position vector
  double* Ry;
  double* Rz;

  double* Rx0; // initial position vectors ( for neighbor list )
  double* Ry0;
  double* Rz0;
  
  double* ux; // unit vector
  double* uy;
  double* uz;
  
  double* Tx; // torque vector
  double* Ty;
  double* Tz;

  double* Fx; // force vector
  double* Fy;
  double* Fz;

  double* Ex; // reaction field
  double* Ey;
  double* Ez;

  double* Axx; // Rotation matrix
  double* Axy;
  double* Axz;

  double* Ayx;
  double* Ayy;
  double* Ayz;

  double* Azx;
  double* Azy;
  double* Azz;
  
  double* epslon; // the array of VDW/LJ epslons
  double* sigma; // the array of VDW/LJ sigmas
  double* mu;  // the magnitude of the dipole moments;
  
  double rCut;      // the LJ/VDW cutoff radius
  double rListSmall;// the inner shell radius of the Neighbor List
  int maxNab;       // the max number of ab pairs (used by neighbor list)
  double rList;     // the cut off shell for the neighbor list
  int* point;       // the pointer array of the neighbor list
  int* list;        // the list of neighbors
  unsigned short int listUpdate; // boolean to update the neighbor list
 
  unsigned short int* isDipole; // boolean array for dipoles
  unsigned short int* isVDW;   // boolean array for VDW atoms
  unsigned short int* isLJ;   // boolean array for LJ atoms
  unsigned short int* isSSD;   // boolean array for SSD atoms

  double potentialE;

};
#endif
Revision:	115
Committed:	Mon Sep 23 15:13:11 2002 UTC (23 years, 1 month ago)
File size:	2365 byte(s)
Log Message:	This commit was manufactured by cvs2svn to create branch 'serial-branch'.
#	Content
1	#ifndef _LRI_H_
2	#define _LRI_H_
3
4	#include <stdio.h>
5	#include <fstream>
6
7	#include "Atom.hpp"
8	#include "AbstractClasses.hpp"
9	#include "SimInfo.hpp"
10
11	using namespace std;
12
13	class AllLong : public LRI{
14
15	public:
16	AllLong( SimInfo* entry_plug );
17	~AllLong();
18	void calc_forces();
19	double get_potential() {return potentialE;}
20
21	private:
22
23	int nPairs; // the number of excluded pairs
24	int* pairI; // the array of excluded pairs
25	int* pairJ;
26	unsigned short int exclude; // boolean on whether there are any excludes
27
28	int nAtoms; // the number of atoms
29	Atom** atoms; // the array of atom objects
30
31	double boxX; // periodic boundry conditions
32	double boxY;
33	double boxZ;
34
35	int nDipoles; // the number of dipoles in the system
36
37	double rRF; // the reaction field cut off radius
38	double rTaper; // the taper radius of the reaction field
39	double dielectric; // the dielectric constant for the reaction field medium
40
41	double* Rx; // position vector
42	double* Ry;
43	double* Rz;
44
45	double* Rx0; // initial position vectors ( for neighbor list )
46	double* Ry0;
47	double* Rz0;
48
49	double* ux; // unit vector
50	double* uy;
51	double* uz;
52
53	double* Tx; // torque vector
54	double* Ty;
55	double* Tz;
56
57	double* Fx; // force vector
58	double* Fy;
59	double* Fz;
60
61	double* Ex; // reaction field
62	double* Ey;
63	double* Ez;
64
65	double* Axx; // Rotation matrix
66	double* Axy;
67	double* Axz;
68
69	double* Ayx;
70	double* Ayy;
71	double* Ayz;
72
73	double* Azx;
74	double* Azy;
75	double* Azz;
76
77	double* epslon; // the array of VDW/LJ epslons
78	double* sigma; // the array of VDW/LJ sigmas
79	double* mu; // the magnitude of the dipole moments;
80
81	double rCut; // the LJ/VDW cutoff radius
82	double rListSmall;// the inner shell radius of the Neighbor List
83	int maxNab; // the max number of ab pairs (used by neighbor list)
84	double rList; // the cut off shell for the neighbor list
85	int* point; // the pointer array of the neighbor list
86	int* list; // the list of neighbors
87	unsigned short int listUpdate; // boolean to update the neighbor list
88
89	unsigned short int* isDipole; // boolean array for dipoles
90	unsigned short int* isVDW; // boolean array for VDW atoms
91	unsigned short int* isLJ; // boolean array for LJ atoms
92	unsigned short int* isSSD; // boolean array for SSD atoms
93
94	double potentialE;
95
96	};
97	#endif