#define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
#define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */
+#define ATOM_ATTR_VA 0x04 /* visualize this atom */
+#define ATOM_ATTR_VB 0x08 /* visualize the bond of this atom */
#define ATOM_ATTR_1BP 0x10 /* single paricle potential */
#define ATOM_ATTR_2BP 0x20 /* pair potential */
int cells; /* total amount of cells */
double len; /* prefered cell edge length */
double x,y,z; /* the actual cell lengthes */
+#ifdef STATIC_LISTS
+ int **subcell; /* pointer to the cell lists */
+#else
t_list *subcell; /* pointer to the cell lists */
+#endif
int dnlc; /* direct neighbour lists counter */
} t_linkcell;
+#define MAX_ATOMS_PER_LIST 20
+
/* moldyn schedule structure */
typedef struct s_moldyn_schedule {
int count;
double cutoff; /* cutoff radius */
double cutoff_square; /* square of the cutoff radius */
double nnd; /* nearest neighbour distance (optional) */
+ double bondlen[3]; /* bond lengthes (only 2 atomic systems) */
t_linkcell lc; /* linked cell list interface */
int set_int_alg(t_moldyn *moldyn,u8 algo);
int set_cutoff(t_moldyn *moldyn,double cutoff);
+int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm);
int set_temperature(t_moldyn *moldyn,double t_ref);
int set_pressure(t_moldyn *moldyn,double p_ref);
int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc);
int scale_velocity(t_moldyn *moldyn,u8 equi_init);
double virial_sum(t_moldyn *moldyn);
double pressure_calc(t_moldyn *moldyn);
-int energy_fluctuation_calc(t_moldyn *moldyn);
+int average_reset(t_moldyn *moldyn);
+int average_and_fluctuation_calc(t_moldyn *moldyn);
int get_heat_capacity(t_moldyn *moldyn);
double thermodynamic_pressure_calc(t_moldyn *moldyn);
double get_pressure(t_moldyn *moldyn);
int link_cell_init(t_moldyn *moldyn,u8 vol);
int link_cell_update(t_moldyn *moldyn);
+#ifdef STATIC_LISTS
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
+#else
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
+#endif
int link_cell_shutdown(t_moldyn *moldyn);
typedef int (*set_hook)(void *,void *);
int moldyn_bc_check(t_moldyn *moldyn);
+int moldyn_read_save_file(t_moldyn *moldyn,char *file);
+int moldyn_load(t_moldyn *moldyn);
int get_line(int fd,char *line,int max);
-int visual_init(t_visual *v,char *filebase);
-int visual_atoms(t_visual *v,double time,t_atom *atom,int n);
+int pair_correlation_init(t_moldyn *moldyn,double dr);
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
+
+int visual_init(t_moldyn *moldyn,char *filebase);
+int visual_atoms(t_moldyn *moldyn);
#endif