t_3dvec f; /* forces */
int element; /* number of element in pse */
double mass; /* atom mass */
+ //t_list vicinity /* verlet neighbour list */
} t_atom;
typedef struct s_moldyn {
double (*potential)(struct s_moldyn *moldyn);
void *pot_params;
int (*force)(struct s_moldyn *moldyn);
+ double cutoff;
double cutoff_square;
t_3dvec dim;
int (*integrate)(struct s_moldyn *moldyn);
int time_steps;
double tau;
void *visual;
+ int write;
unsigned char status;
} t_moldyn;
+typedef struct s_ho_params {
+ double spring_constant;
+ double equilibrium_distance;
+} t_ho_params;
+
typedef struct s_lj_params {
double sigma6;
double sigma12;
/* phsical values */
-//#define K_BOLTZMANN 1.3807E-23
-#define K_BOLTZMANN 1.0
+#define K_BOLTZMANN 1.3807e-27 /* Nm/K */
+#define AMU 1.660540e-27 /* kg */
#define FCC 0x01
#define DIAMOND 0x02
#define C 0x06
-#define M_C 6.0
+#define M_C (12.011*AMU)
-#define Si 0x0e
-#define M_SI 14.0
-#define LC_SI 5.43105
+#define SI 0x0e
+#define LC_SI 0.543105e-9 /* m */
+#define M_SI (28.085*AMU) /* kg */
+#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
+#define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
/* function prototypes */
double get_total_energy(t_moldyn *moldyn);
t_3dvec get_total_p(t_atom *atom,int count);
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+
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);