t_3dvec dim; /* dimensions of the simulation volume */
/* potential force function and parameter pointers */
- int (*pf_func1b)(struct s_moldyn *,t_atom *);
+ int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
void *pot1b_params;
- int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+ int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
void *pot2b_params;
- int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+ int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
+ u8 bck);
void *pot3b_params;
//int (*potential_force_function)(struct s_moldyn *moldyn);
int (*integrate)(struct s_moldyn *moldyn);
int time_steps; /* amount of iterations */
double tau; /* delta t */
+ double time; /* absolute time */
double tau_square; /* delta t squared */
double elapsed; /* total elapsed time */
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_PBX 0x08 /* periodic boudaries in x */
#define MOLDYN_STAT_PBY 0x10 /* y */
#define MOLDYN_STAT_PBZ 0x20 /* and z direction */
/* tersoff exchange structure to exchange 2bp and 3bp calculated values */
typedef struct s_tersoff_exchange {
double f_c,df_c;
+ double f_a,df_a;
t_3dvec dist_ij;
double d_ij;
double h[2];
t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
-} t_tersoff_params;
+} t_tersoff_mult_params;
#define MOLDYN_CUTOFF 1.0e-9
#define MOLDYN_RUNS 1000000
+#define MOLDYN_CRITICAL_EST_TEMP 5.0
+
#define MOLDYN_INTEGRATE_VERLET 0x00
#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
#define MOLDYN_POTENTIAL_LJ 0x01
#define MOLDYN_POTENTIAL_TM 0x02
-#define MOLDYN_SET_POTENTIAL 0x00
-#define MOLDYN_SET_TEMPERATURE 0x01
-#define MOLDYN_SET_
-#define MOLDYN_SET_
+#define LOG_TOTAL_ENERGY 0x01
+#define LOG_TOTAL_MOMENTUM 0x02
+#define SAVE_STEP 0x04
+#define VISUAL_STEP 0x08
#define TRUE 1
#define FALSE 0
*
*/
+typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
+typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
+typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
+
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
int set_temperature(t_moldyn *moldyn,double t);
int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
-int set_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params);
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
-nt moldyn_log_shutdown(t_moldyn *moldyn);
+int moldyn_log_shutdown(t_moldyn *moldyn);
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
u8 attr,u8 bnum,int a,int b,int c);
int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
- t_3dvec r,t_3dvec v);
+ t_3dvec *r,t_3dvec *v);
int destroy_atoms(t_moldyn *moldyn);
int thermal_init(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
t_3dvec get_total_p(t_moldyn *moldyn);
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+double estimate_time_step(t_moldyn *moldyn,double nn_dist);
int link_cell_init(t_moldyn *moldyn);
int link_cell_update(t_moldyn *moldyn);
int potential_force_calc(t_moldyn *moldyn);
int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_Atom *aj,u8 bc);
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);