X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=c6712ba41d1508fb8e359b627c71082e1307567a;hb=0d71b08d4382b23b8217342caf138cfce36226cc;hp=49ca0b28f92133cedf8da5ee7831734f5892da17;hpb=e763f6e3072fbbbc5ecf7345b989d7d29929a38f;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 49ca0b2..c6712ba 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,35 +12,50 @@
 #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 */
 } t_linkcell;
 
 #include "visual/visual.h"
 
+# moldyn properties structure */
+
 typedef struct s_moldyn {
-	/* atoms, amount, dimensions */
-	int count;
-	t_atom *atom;
-	t_3dvec dim;
+
+	int count;		/* total amount of atoms */
+	t_atom *atom;		/* pointer to the atoms */
+	t_3dvec dim;		/* dimensions of the simulation volume */
 	/* potential, force & parameters */
+
+	/* potential force funtion created by the user */
 	int (*potential_force_function)(struct s_moldyn *moldyn);
-	void *pot_params;
-	/* cut off radius */
+	void *pot_params;	/* parameters describing the potential */ 
+
 	double cutoff;
 	double cutoff_square;
 	/* linked list / cell method */