Crystal(API)

General/Crystal is API for Crystal Structure.

constant

Crystal Structure

Use as value of CrystalInfo->SpaceGroup.

typedef enum CrystalSpaceGroup {
	CrystalSpaceGroupP1=0,
	CrystalSpaceGroupHelical=1
} CrystalSpaceGroup;

#ifdef __CRYSTALINIT__ 
char* CrystalSpaceGroupString[] = {
	"P1",
	"HelicalSymmmetry",
	NULL	
};
#else
extern char* CrystalSpaceGroupString[];
#endif

struct

typedef float CrystalParaTypeReal;
typedef int   CrystalParaTypeInteger;

typedef struct CrystalParaTypeRealCoord {
	CrystalParaTypeReal x;
	CrystalParaTypeReal y;
	CrystalParaTypeReal z;
} CrystalParaTypeRealCoord;

typedef struct CrystalParaTypeIntegerCoord {
	CrystalParaTypeInteger x;
	CrystalParaTypeInteger y;
	CrystalParaTypeInteger z;
} CrystalParaTypeIntegerCoord;

typedef struct CrystalParaTypeRealAxis {
	CrystalParaTypeReal a;
	CrystalParaTypeReal b;
	CrystalParaTypeReal c;
} CrystalParaTypeRealAxis;

typedef struct CrystalParaTypeIntegerAxis {
	CrystalParaTypeInteger a;
	CrystalParaTypeInteger b;
	CrystalParaTypeInteger c;
} CrystalParaTypeIntegerAxis;

typedef struct HelicalSymmetryInfo {
	CrystalParaTypeInteger t;         /* Turn */
	CrystalParaTypeInteger u;         /* Unit */ 
	CrystalParaTypeInteger n;         /* n-strands */

	/* 
		Don't change the below variables directly,
		bacause the variables can be calculated by the upper's.
	*/
	CrystalParaTypeReal    dz;     /* dz     = TruePitch/unit */
	CrystalParaTypeReal    dphi;   /* dphi   = 2*PI*turn/unit */
} HelicalSymmetryInfo;

typedef struct CrystalInfo {
	CrystalParaTypeRealCoord    aAxis;    /* Unit Cell Vector : a-axis : Length = 1 */
	CrystalParaTypeRealCoord    bAxis;    /* Unit Cell Vector : b-axis : Length = 1 */
	CrystalParaTypeRealCoord    cAxis;    /* Unit Cell Vector : c-axis : Length = 1 */
	CrystalParaTypeRealAxis     CellLength;    /* Unit Cell Size   a, b, c-axis [A] */
	CrystalParaTypeRealCoord    Origin;        /* Unit Cell Origin [A] */
	CrystalParaTypeIntegerAxis  N;             /* Number of Unit Cells a, b, c-axis */
	CrystalParaTypeIntegerAxis  StartN;        /* Start  of Unit Cells a, b, c-axis */
	CrystalSpaceGroup           SpaceGroup;
	
	/* Information for Special Symmetry */
	HelicalSymmetryInfo HelixInfo;
		/* For HelicalSymmetry : 
			The filament axis (z-axis) is treated as the c-axis. 
			The azimuthal axis (phi-axis) is treated as the b-axis. 
			The radius axis (r-axis) is treated as the a-axis.
		*/
} CrystalInfo;

API

Initialize

Initialize crystal.

extern void crystalInit(CrystalInfo* crystal);

File Read

Read data in file fpt, and store to linfo.

extern void crystalInfoRead(FILE* fpt, CrystalInfo* linfo, int mode);

File Write

Write data of linfo to file fpt.

extern void crystalInfoWrite(FILE* fpt, CrystalInfo* linfo, int mode);

Set length of axis

Set the length of specified axis in C.
In addition, recalculate its coordinates by using crystalAxisSetUsingCellLength.

extern void crystalCellLengthSet(CrystalInfo* C, char axis, CrystalParaTypeReal length, int mode);

Calculate coordinates of specified axis, and store to C->pAxis.x(p=a, b, c).

extern void crystalAxisSetUsingCellLength(CrystalInfo* C, char axis, int mode);

Set coordinates of axis

Set the coordinates of specified axis in C.
In addition, recalculate its length by using crystalCellLengthSetUsingAxis.

extern void crystalAxisSet(CrystalInfo* C, char axis, CrystalParaTypeReal x, CrystalParaTypeReal y, CrystalParaTypeReal z, int mode);

Calculate length of specified axis, and store to C->CellLength.p(p=a, b, c).

extern void crystalCellLengthSetUsingAxis(CrystalInfo* C, char axis, int mode);

APIInformation

Help

extern void crystalInfoFileFormat(FILE* fpt, int mode);

Output useable crystal structure to fpt.(List: CrystalSpaceGroupString)

extern void crystalSpaceGroupPrint(FILE* fpt, int mode);