X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=717388abf58e080dd0ceab4539ee4fbbf3dc295d;hb=06912ca45b46de412570a4bd5b5484aa9e8d6e6b;hp=49ca0b28f92133cedf8da5ee7831734f5892da17;hpb=2a902b8d09fd57bc20681448774e2f93894f10aa;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 49ca0b2..717388a 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,72 +12,100 @@
 #include "random/random.h"
 #include "list/list.h"
 
+
 /* datatypes */
 
+
+/* the atom of the md simulation */
+
 typedef struct s_atom {
-	t_3dvec r;	/* positions */
-	t_3dvec v;	/* velocities */
-	t_3dvec f;	/* forces */
-	int element;	/* number of element in pse */
-	double mass;	/* atom mass */
+	t_3dvec r;		/* position */
+	t_3dvec v;		/* velocity */
+	t_3dvec f;		/* force */
+	int element;		/* number of element in pse */
+	double mass;		/* atom mass */
+	unsigned char attr;	/* attributes */
 } t_atom;
 
+#define ATOM_ATTR_FP	0x01	/* fixed position (bulk material) */
+#define ATOM_ATTR_HB	0x02	/* coupled to heat bath (velocity scaling) */
+
+/* cell lists */
+
 typedef struct s_linkcell {
-	int listfd;
-	int nx,ny,nz;
-	int cells;
-	double x,y,z;
-	t_list *subcell;
+	int nx,ny,nz;		/* amount of cells in x, y and z direction */
+	int cells;		/* total amount of cells */
+	double len;		/* prefered cell edge length */
+	double x,y,z;		/* the actual cell lengthes */
+	t_list *subcell;	/* pointer to the cell lists */
+	int dnlc;		/* direct neighbour lists counter */
+	int countn;		/* amount of neighbours */
 } t_linkcell;
 
 #include "visual/visual.h"
 
+# moldyn structure */
+
 typedef struct s_moldyn {
-	/* atoms, amount, dimensions */
-	int count;
-	t_atom *atom;
-	t_3dvec dim;
-	/* potential, force & parameters */
-	int (*potential_force_function)(struct s_moldyn *moldyn);
-	void *pot_params;
-	/* cut off radius */
-	double cutoff;
-	double cutoff_square;
-	/* linked list / cell method */
-	t_linkcell lc;
-	/* temperature */
-	double t;
-	/* integration of newtons equations */
+
+	int count;		/* total amount of atoms */
+	t_atom *atom;		/* pointer to the atoms */
+
+	t_3dvec dim;		/* dimensions of the simulation volume */
+
+	/* potential force function pointer and parameters */
+	int (*pf_func1b)(struct s_moldyn *,t_atom *);
+	int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+	int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+	//int (*potential_force_function)(struct s_moldyn *moldyn);
+	void *pot_params;	/* parameters describing the potential */ 
+
+	double cutoff;		/* cutoff radius */
+	double cutoff_square;	/* square of the cutoff radius */
+
+	t_linkcell lc;		/* linked cell method */
+
+	double t;		/* temperature */
+
+	/* integration function pointer */
 	int (*integrate)(struct s_moldyn *moldyn);
-	int time_steps;
-	double tau;
-	double tau_square;
-	/* energy */
-	double energy;
-	/* logging & visualization */
-	t_visual vis;
-	unsigned char lvstat;
-	unsigned int ewrite;
-	char efb[64];
-	int efd;
-	unsigned int mwrite;
-	char mfb[64];
-	int mfd;
-	unsigned int swrite;
-	char sfb[64];
-	int sfd;
-	unsigned int dwrite;
-	char dfb[64];
-	int dfd;
-	unsigned int vwrite;
-	char vfb[64];
-	void *visual;
-	/* moldyn general status */
-	unsigned char status;
-	/* random */
-	t_random random;
+	int time_steps;		/* amount of iterations */
+	double tau;		/* delta t */
+	double tau_square;	/* delta t squared */
+
+	double energy;		/* energy */
+
+	t_visual vis;		/* visualization/log/save interface structure */
+	unsigned char lvstat;	/* log & vis properties */
+	unsigned int ewrite;	/* how often to log energy */
+	char efb[64];		/* energy log filename */
+	int efd;		/* fd for energy log */
+	unsigned int mwrite;	/* how often to log momentum */
+	char mfb[64];		/* momentum log filename */
+	int mfd;		/* fd for momentum log */
+	unsigned int vwrite;	/* how often to visualize atom information */
+	char vfb[64];		/* visualization file name base */
+	void *visual;		/* pointer (hack!) */
+	unsigned int swrite;	/* how often to create a save file */
+
+	unsigned char status;	/* general moldyn properties */
+
+	t_random random;	/* random interface */
 } t_moldyn;
 
+#define MOLDYN_LVSTAT_TOTAL_E		0x01
+#define MOLDYN_LVSTAT_TOTAL_M		0x02
+#define MOLDYN_LVSTAT_SAVE		0x04
+#define MOLDYN_LVSTAT_VISUAL		0x08
+#define MOLDYN_LVSTAT_INITIALIZED	0x10
+
+#define MOLDYN_STAT_1BP			0x01
+#define MOLDYN_STAT_2BP			0x02	/* define for pair potentials */
+#define MOLDYN_STAT_3BP			0x04	/* define for 3 body pot */ 
+#define MOLDYN_STAT_PBX			0x08	/* periodic boudaries in x */
+#define MOLDYN_STAT_PBY			0x10	/* y */
+#define MOLDYN_STAT_PBZ			0x20	/* and z direction */
+
 typedef struct s_ho_params {
 	double spring_constant;
 	double equilibrium_distance;
@@ -104,27 +132,17 @@ typedef struct s_tersoff_params {
 
 /* general defines */
 
-#define MOLDYN_LVSTAT_TOTAL_E		0x01
-#define MOLDYN_LVSTAT_TOTAL_M		0x02
-#define MOLDYN_LVSTAT_SAVE		0x04
-#define MOLDYN_LVSTAT_DUMP		0x08
-#define MOLDYN_LVSTAT_VISUAL		0x10
-#define MOLDYN_LVSTAT_INITIALIZED	0x80
-
-#define MOLDYN_STAT_POTENTIAL		0x01
-#define MOLDYN_STAT_FORCE		0x02
-
 #define MOLDYN_TEMP			273.0
 #define MOLDYN_TAU			1.0e-15
 #define MOLDYN_CUTOFF			10.0e-9
 #define MOLDYN_RUNS			1000000
 
 #define MOLDYN_INTEGRATE_VERLET		0x00
-#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+#define MOLDYN_INTEGRATE_DEFAULT 	MOLDYN_INTEGRATE_VERLET
 
 #define MOLDYN_POTENTIAL_HO		0x00
 #define MOLDYN_POTENTIAL_LJ		0x01
-#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+#define MOLDYN_POTENTIAL_DEFAULT 	MOLDYN_POTENTIAL_LJ
 
 /* phsical values */