#include "visual/visual.h"
-# moldyn schedule structure */
+/* moldyn schedule structure */
typedef struct s_moldyn_schedule {
int content_count;
int *runs;
- int *tau;
- int (*hook)(t_moldyn *,void *);
+ double *tau;
+ int (*hook)(void *moldyn,void *hook);
void *hook_params;
} t_moldyn_schedule;
double tau_square; /* delta t squared */
double elapsed; /* total elapsed time */
- double energy; /* energy */
+ double energy; /* potential energy */
+ double ekin; /* kinetic energy */
t_visual vis; /* visualization/log/save interface structure */
u8 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 */
+ char sfb[64]; /* visualization file name base */
u8 status; /* general moldyn properties */
#define MOLDYN_STAT_PBY 0x10 /* y */
#define MOLDYN_STAT_PBZ 0x20 /* and z direction */
+#define MOLDYN_1BP 0x00
+#define MOLDYN_2BP 0x01
+#define MOLDYN_3BP 0x02
+
/*
*
#define MOLDYN_SET_
#define MOLDYN_SET_
+#define TRUE 1
+#define FALSE 0
+
/*
*
* phsical values / constants
*
*/
-int moldyn_usage(char **argv);
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn);
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
-int create_lattice(u8 type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom);
-int destroy_lattice(t_atom *atom);
+int set_int_alg(t_moldyn *moldyn,u8 algo);
+int set_cutoff(t_moldyn *moldyn,double cutoff);
+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 moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
+nt 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);
+int destroy_atoms(t_moldyn *moldyn);
+
int thermal_init(t_moldyn *moldyn);
int scale_velocity(t_moldyn *moldyn);
-double get_e_kin(t_atom *atom,int count);
+
+double get_e_kin(t_moldyn *moldyn);
double get_e_pot(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
-t_3dvec get_total_p(t_atom *atom,int count);
+t_3dvec get_total_p(t_moldyn *moldyn);
double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
int link_cell_shutdown(t_moldyn *moldyn);
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau);
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params);
+
int moldyn_integrate(t_moldyn *moldyn);
int velocity_verlet(t_moldyn *moldyn);
-int harmonic_oscillator(t_moldyn *moldyn);
-int lennard_jones(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 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);
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
#endif