particle.h

一个很好的分子动力学程序

#ifndef __PARTICLE_H
#define __PARTICLE_H
/*
	 8 Oct 91 : added member to particle structure "rmin" for use by
					bond.c  (bond.c calculates number of atoms with bond
					between rmin and cutoff).
*/

/*
***********************************************************************
Defines
***********************************************************************
*/

#define TRUE 1
#define FALSE 0

#define X 0
#define Y 1
#define Z 2
#define NDIR 3

#define WORD	 unsigned int
#define BYTE	 unsigned char
#define USHORT  unsigned short int
#define BOOLEAN int
#define COORD	 double (*)[NDIR]

/*  Voight constants  */
#define XX 0
#define YY 1
#define ZZ 2
#define YZ 3
#define ZX 4
#define XY 5
#define ZY 3
#define XZ 4
#define YX 5
#define NVOIGHT 6

/*  LENGTH OF TITLE STRING  */
#define NTITLESTR 81

/*  Different type of dynamic volume conditions */
#define BMG_ISOTROPIC	0
#define BMG_ORTHONORMAL 1
#define BMG_MONOCLINIC	2

/*  Constant pressure algorithms  */
#define BMA_NONE			0
#define BMA_ANDERSEN 	1
#define BMA_MODIFIED 	2

/*  Repeating boundary geometries */
#define BD_ORTHONORMAL	1		/*  Standard box boundary			 */
#define BD_MONOCLINIC	2		/*  Parallel-piped boundary		 */
#define BC_ARC 			3		/*  Curved "race track" boundary  */

/*  Define number of derivatives in Gear algorithm  */
#define NDERIV 6

/*  Maximum number of type names  */
#define MAX_TYPE_NAMES 32

/*  Constants for using Selection bit fields  */

/*  Number of reserved Selection bit fields  */
#define NUM_RESERVED_SELECTION_FIELDS 3

/*  Number of available set bit fields  */
#define MAX_SET     13

/*  Selection Bit Masks  */
#define MASK_SELECT 0x8000  
#define MASK_FIXED  0x4000 
#define MASK_CLAMP  0x2000




/*
************************************************************************
Macros
************************************************************************
*/
#define IS_SELECT(INDEX)     (a->Selection[INDEX] &   MASK_SELECT)
#define REMOVE_SELECT(INDEX) {a->Selection[INDEX] &= ~MASK_SELECT;}
#define APPLY_SELECT(INDEX)  {a->Selection[INDEX] |=  MASK_SELECT;}

#define IS_FIXED(INDEX)     (a->Selection[INDEX] &   MASK_FIXED)
#define REMOVE_FIXED(INDEX) {a->Selection[INDEX] &= ~MASK_FIXED;}
#define APPLY_FIXED(INDEX)  {a->Selection[INDEX] |=  MASK_FIXED;}

#define IS_CLAMP(INDEX)     (a->Selection[INDEX] &   MASK_CLAMP)
#define REMOVE_CLAMP(INDEX) {a->Selection[INDEX] &= ~MASK_CLAMP;}
#define APPLY_CLAMP(INDEX)  {a->Selection[INDEX] |=  MASK_CLAMP;}

#define IS_SET(INDEX,SET)     (a->Selection[INDEX] &   (1 << (SET-1)))
#define REMOVE_SET(INDEX,SET) {a->Selection[INDEX] &= ~(1 << (SET-1));}
#define APPLY_SET(INDEX,SET)  {a->Selection[INDEX] |=  (1 << (SET-1));}




/*
************************************************************************
Type Definitions
************************************************************************
*/

/*  Particle constaint	*/
typedef struct
	{
	double xd,yd,zd, xp,yp,zp;  /*  POINT AND DIRECTION					*/
	int	 type;					 /*  TYPE OF CONSTRAIN 0-line 1-Plane	*/
	}
	Constraint_t;

/*
External vector and coordinate origin storage
Used for both external force and spring
*/
typedef struct
	{
	double Origin[NDIR];
	double Vector[NDIR];
	}
	ExternalVector_t;

/*  Particle Information  */
typedef struct
	{

	/*  Particle Coordinate arrays  */
	double  *cur, *ref, *ngh;				/*  current, origin, neighbor 		*/
	double  *v, *f;							/*  velocity, force						*/
	double  *c2,*c3,*c4,*c5;				/*  gear integration values			*/
	double  *disp; 							/*  Particle displacements 			*/

	/*  Particle Misc Info	*/
	double  *mass; 							/*  mass/atom								*/
	double  *eatom;							/*  energy/atom							*/
	BYTE	  *type, *rtype;					/*  type 									*/

	/*  Constraints  */
	Constraint_t **cons; 					/*  constraint 							*/
	double  CavityCenter[NDIR];
	double  CavityAxis  [NDIR];
	double  CavitySpring;
	BOOLEAN UseCavity;
	/*  Particle Status Arrays  */
	BYTE	  *tag;
/*
	BYTE	  *sel, *tag, *set, *fix;
*/
	USHORT  *Selection;

	/*  Type Names (such as "Fe", "Na", etc)  */
	char	  *TypeNames[MAX_TYPE_NAMES];

	double  bcur [NDIR];
	double  bref [NDIR];
	double  trans[NDIR];


	/*  Array storing poiners to external force and spring info */
	ExternalVector_t **SpringPtrList;
	ExternalVector_t **ForcePtrList;

	/*  Array storing damping coefficient   */
	BOOLEAN UseDamp;
	double *Damp;

	/*  Array for storing neighbor list  */
	int	  *NeighborListIndex;
	int	  *NeighborListLength;
	USHORT  *NeighborList;
	int     TotalNumNeighbors;

	/*  Flags */
	BOOLEAN	boxflag, coordflag, selkeep;

	/*  Neighbor List Flag	*/
	BOOLEAN InvalidNeighborList;

	/*  Neighbor Type Flag  */
	BOOLEAN CalcUniqueNeighbors;

	/*  Surface Flag	*/
	int	  surf[3];

	/*  Lattice Energies  */
	double  ebath, etot, temp, epot, ekin;

	/*  Average potential energy (used by cdmc.c)  */
	double  epavg;
	long	  navg;

	/*  Internal Stresses  */
	double Stress[NVOIGHT];

	/*  Variables needed for changing volume	*/
	int	 BoxMotionGeometry;	  /*	Either isotropic, othrnormal or monoclinic  */
	int	 BoxMotionAlgorithm;   /*	Either NONE, ANDERSEN, MODIFIED				  */
	double Pressure;
	double EkinBox  [NDIR];
	double EpotBox;
	double BoxMotion[NDIR][NDERIV];
	double BoxForce [NDIR];
	double BoxMass  [NDIR];

	/*  Repeating Boundary Geometry	*/
	int	 BoundaryType;

	/*  If using monoclinic boundary type, then need metric	*/
	double BoundaryMetric	[NDIR][NDIR];
	double BoundaryInvMetric[NDIR][NDIR];

	/*  Number of particles  */
	int	  np;

	/*  Number of neighbors  */
	int	  ng;

	/*  Number of selected particles  */
	int	  nsel;

	/*  Number of fixed particles   */
	int	  nfix;
	int	  nbin;
	char	  title[8][NTITLESTR];
	long	  run, step;
	int	  ndim;
	double  time, tempc, dtime, size, cutoff, rmin, vibp;
	double  rdftable[100];

	/*  Arrays for xmdview  */
	WORD *DepthIndex;


	}
	Particle_t;

#endif