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 SEL_T   unsigned short
#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_ORTHORHOMBIC 1
#define BMG_MONOCLINIC   2

/*  Constant pressure algorithms  */
#define BMA_NONE        0
#define BMA_ANDERSEN    1
#define BMA_CLAMP       2
#define BMA_MODIFIED    3

/*  Repeating boundary geometries */
#define BD_ORTHORHOMBIC 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

/*  Selection values  */
#define MAX_SET     12
#define MASK_SELECT 0x8000
#define MASK_FIX    0x4000
#define MASK_CLAMP  0x3000

#define NUM_CLAMP_TAG 4




/*
************************************************************************
Macros
************************************************************************
*/
#define CLEAR_ALL_FLAGS(INDEX) {a->Selection[INDEX]=0;}

#define IS_SELECT(INDEX)     ((a->Selection[INDEX] &   MASK_SELECT)!=0)
#define REMOVE_SELECT(INDEX) {a->Selection[INDEX] &= ~MASK_SELECT;}
#define APPLY_SELECT(INDEX)  {a->Selection[INDEX] |=  MASK_SELECT;}

#define IS_SELECT2(SEL,INDEX)     ((SEL[INDEX] &   MASK_SELECT)!=0)
#define APPLY_SELECT2(SEL,INDEX)  {SEL[INDEX] |=  MASK_SELECT;}
#define REMOVE_SELECT2(SEL,INDEX) {SEL[INDEX] &= ~MASK_SELECT;}

#define IS_FIX(INDEX)       ((a->Selection[INDEX] &   MASK_FIX)!=0)
#define REMOVE_FIX(INDEX)  {a->Selection[INDEX] &= ~MASK_FIX;}
#define APPLY_FIX(INDEX)  {a->Selection[INDEX] |=  MASK_FIX;}

#if 0
#define IS_CLAMP(INDEX)     ((a->Selection[INDEX] &   MASK_CLAMP1)!=0)
#define REMOVE_CLAMP(INDEX) {a->Selection[INDEX] &= ~MASK_CLAMP1;}
#define APPLY_CLAMP(INDEX)  {a->Selection[INDEX] |=  MASK_CLAMP1;}
#endif


#define IS_CLAMP_TAG(INDEX,TAG) \
   ((a->Selection[INDEX] & MASK_CLAMP)==(TAG<<MAX_SET))

#define APPLY_CLAMP_TAG(INDEX,TAG) \
{ \
a->Selection[INDEX] &=  ~MASK_CLAMP; \
a->Selection[INDEX] |=  (TAG << MAX_SET); \
}

#define GET_CLAMP_TAG(INDEX) \
((a->Selection[INDEX] & MASK_CLAMP) >> MAX_SET)


#define IS_SET(INDEX,SET)   ((a->Selection[INDEX] &   (1<<(SET-1)))!=0)
#define REMOVE_SET(INDEX,SET)  {a->Selection[INDEX] &= ~(1 << (SET-1));}
#define APPLY_SET(INDEX,SET)  {a->Selection[INDEX] |=  (1 << (SET-1));}




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

/*
 * At some point use this to replace some double * types  May 19, 1998
 *
*/
/*  Coordinate type  */
typedef double Coord_t[NDIR];

/*  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;
#if 0
   BYTE    *sel, *tag, *set, *fix;
#endif
   SEL_T   *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;
   int     *NeighborList;
   int     TotalNumNeighbors;

   /*  Initialization flag  */
   BOOLEAN IsInitializedBox;
   BOOLEAN IsInitializedCoord;
   BOOLEAN IsInitializedMass;
   BOOLEAN IsInitializedPotential;
   BOOLEAN IsInitializedSurface;
   BOOLEAN selkeep;
#if 0
   /*  Flags */
   BOOLEAN  boxflag, coordflag, selkeep;
#endif

   /*  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  */
   /*  Either isotropic, othrnormal or monoclinic  */
   int     BoxMotionGeometry;   
   /* Either BMA_NONE, ..ANDERSEN, ..CLAMP */
   int     BoxMotionAlgorithm;   
   double  Pressure [NDIR];
   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];

   /*  Clamp info  */
   BOOLEAN UseClamp [NUM_CLAMP_TAG];
   double  ClampTemp[NUM_CLAMP_TAG];
   double  ClampStep[NUM_CLAMP_TAG];

	/*  Volume clamp info  */
	double  VolClampStep;
	double  BulkModulus;

   /*  Allocation info  */
   WORD NumNeighAlloc;
   WORD NumPartAlloc;

	/*  Degrees of freedom  */
	int DegFree;

	/*  Thermal stress switch  */
   BOOLEAN stress_thermal;

   }
   Particle_t;

#endif