/* the atom of the md simulation */
typedef struct s_atom {
+ t_3dvec r_0; /* initial position */
t_3dvec r; /* position */
t_3dvec v; /* velocity */
t_3dvec f; /* force */
t_virial virial; /* virial */
double e; /* site energy */
+ double ekin; /* kinetic energy */
int element; /* number of element in pse */
double mass; /* atom mass */
u8 brand; /* brand id */
/* moldyn main structure */
typedef struct s_moldyn {
+ int argc; /* number of arguments */
+ char **args; /* pointer to arguments */
+
int count; /* total amount of atoms */
double mass; /* total system mass */
t_atom *atom; /* pointer to the atoms */
double t_sum; /* sum over all t */
double t_avg; /* average value of t */
- t_virial virial; /* global virial (absolute coordinates) */
+ t_virial gvir; /* global virial (absolute coordinates) */
+ double gv;
+ double gv_sum;
+ double gv_avg;
+
double gp; /* pressure computed from global virial */
double gp_sum; /* sum over all gp */
double gp_avg; /* average value of gp */
- double virial_avg; /* average of virial */
+ double virial; /* actual virial */
double virial_sum; /* sum over all calculated virials */
+ double virial_avg; /* average of virial */
double p_ref; /* reference pressure */
double p; /* actual pressure (computed by virial) */
double p_sum; /* sum over all p */
double p_avg; /* average value of p */
+
t_3dvec tp; /* thermodynamic pressure dU/dV */
double dv; /* dV for thermodynamic pressure calc */
#define ALBE_LC_C 3.566
#define ALBE_R_SIC (2.40-0.20)
-#define ALBE_S_SIC (2.40+0.10)
+#define ALBE_S_SIC (2.40+0.20)
#define ALBE_A_SIC (4.36*EV/0.847)
#define ALBE_B_SIC (1.847*4.36*EV/0.847)
#define ALBE_R0_SIC 1.79
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+ t_3dvec *r,t_3dvec *v);
int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
- t_3dvec *r,t_3dvec *v);
int destroy_atoms(t_moldyn *moldyn);
int thermal_init(t_moldyn *moldyn,u8 equi_init);
double temperature_calc(t_moldyn *moldyn);
double get_temperature(t_moldyn *moldyn);
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 get_heat_capacity(t_moldyn *moldyn);