began rewrite ...

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index 49ca0b2..c6712ba 100644 (file)
--- 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 */