t_3dvec r; /* positions */
t_3dvec v; /* velocities */
t_3dvec f; /* forces */
- t_3dvec dr; /* delta r for verlet list updates */
int element; /* number of element in pse */
double mass; /* atom mass */
- t_list verlet; /* verlet neighbour list */
} t_atom;
typedef struct s_linkcell {
t_atom *atom;
t_3dvec dim;
/* potential, force & parameters */
- double (*potential)(struct s_moldyn *moldyn);
- int (*force)(struct s_moldyn *moldyn);
+ int (*potential_force_function)(struct s_moldyn *moldyn);
void *pot_params;
- /* cut off radius, verlet list & co */
+ /* cut off radius */
double cutoff;
double cutoff_square;
- double r_verlet;
- double dr_max1;
- double dr_max2;
/* linked list / cell method */
t_linkcell lc;
/* temperature */
int (*integrate)(struct s_moldyn *moldyn);
int time_steps;
double tau;
+ double tau_square;
+ /* energy */
+ double energy;
/* logging & visualization */
unsigned char lvstat;
unsigned int ewrite;
#define MOLDYN_TAU 1.0e-15
#define MOLDYN_RUNS 1000000
+#define MOLDYN_INTEGRATE_VERLET 0x00
+#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET
+
+#define MOLDYN_POTENTIAL_HO 0x00
+#define MOLDYN_POTENTIAL_LJ 0x01
+#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ
+
/* phsical values */
#define K_BOLTZMANN 1.3807e-27 /* Nm/K */
int create_lattice(unsigned char type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom);
int destroy_lattice(t_atom *atom);
-int thermal_init(t_moldyn *moldyn,t_random *random,int count);
-int scale_velocity(t_moldyn *moldyn,int count);
+int thermal_init(t_moldyn *moldyn,t_random *random);
+int scale_velocity(t_moldyn *moldyn);
double get_e_kin(t_atom *atom,int count);
double get_e_pot(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
-int verlet_list_init(t_moldyn *moldyn);
int link_cell_init(t_moldyn *moldyn);
-int verlet_list_update(t_moldyn *moldyn);
int link_cell_update(t_moldyn *moldyn);
-int verlet_list_shutdown(t_moldyn *moldyn);
+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_integrate(t_moldyn *moldyn);
int velocity_verlet(t_moldyn *moldyn);
-double potential_harmonic_oscillator(t_moldyn *moldyn);
-int force_harmonic_oscillator(t_moldyn *moldyn);
-double potential_lennard_jones(t_moldyn *moldyn);
-int force_lennard_jones(t_moldyn *moldyn);
+int harmonic_oscillator(t_moldyn *moldyn);
+int lennard_jones(t_moldyn *moldyn);
#endif