/* 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 */
t_3dvec dim; /* dimensions of the simulation volume */
t_linkcell lc; /* linked cell list interface */
+ int avg_skip; /* amount of steps without average calc */
+
double t_ref; /* reference temperature */
double t; /* actual temperature */
double t_sum; /* sum over all t */
- double mean_t; /* mean value of t */
+ double t_avg; /* average value of t */
+
+ t_virial gvir; /* global virial (absolute coordinates) */
+ double gv;
+ double gv_sum;
+ double gv_avg;
- t_virial virial; /* global virial (absolute coordinates) */
double gp; /* pressure computed from global virial */
double gp_sum; /* sum over all gp */
- double mean_gp; /* mean value of gp */
+ double gp_avg; /* average value of gp */
- double mean_v; /* mean 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 mean_p; /* mean value of p */
+ double p_avg; /* average value of p */
+
t_3dvec tp; /* thermodynamic pressure dU/dV */
double dv; /* dV for thermodynamic pressure calc */
double ekin; /* kinetic energy */
/* energy averages & fluctuations */
- double k_m;
- double p_m;
- double t_m;
- double dk2_m; /* mean square kinetic energy fluctuations */
- double dp2_m; /* mean square potential energy fluctuations */
- double dt2_m; /* mean square fluctuations in total energy */
+ double k_sum; /* sum of kinetic energy */
+ double v_sum; /* sum of potential energy */
+ double k_avg; /* average of kinetic energy */
+ double v_avg; /* average of potential energy */
+ double k2_sum; /* sum of kinetic energy squared */
+ double v2_sum; /* sum of potential energy squared */
+ double k2_avg; /* average of kinetic energy squared */
+ double v2_avg; /* average of potential energy squared */
+ double dk2_avg; /* mean square kinetic energy fluctuations */
+ double dv2_avg; /* mean square potential energy fluctuations */
/* response functions */
double c_v_nve; /* constant volume heat capacity (nve) */
#define TM_CHI_SIC 0.9776
-#define TM_LC_3C_SIC (0.432e-9*METER) /* A */
+#define TM_LC_SIC 4.32 /* A */
#define ALBE_R_SI (2.82-0.14)
#define ALBE_S_SI (2.82+0.14)
#define ALBE_D_SI 0.81472
#define ALBE_H_SI 0.259
-#define LC_SI_ALBE 5.429
+#define ALBE_LC_SI 5.429
#define ALBE_R_C (2.00-0.15)
#define ALBE_S_C (2.00+0.15)
#define ALBE_D_C 6.28433
#define ALBE_H_C 0.5556
-#define LC_C_ALBE 3.566
+#define ALBE_LC_C 3.566
#define ALBE_R_SIC (2.40-0.20)
#define ALBE_S_SIC (2.40+0.10)
#define ALBE_D_SIC 180.314
#define ALBE_H_SIC 0.68
-#define LC_SIC_ALBE 4.359
+#define ALBE_LC_SIC 4.359
/*
int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
int set_potential_params(t_moldyn *moldyn,void *params);
+int set_avg_skip(t_moldyn *moldyn,int skip);
+
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
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 total_mass_calc(t_moldyn *moldyn);
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);
double thermodynamic_pressure_calc(t_moldyn *moldyn);
double get_pressure(t_moldyn *moldyn);
int scale_volume(t_moldyn *moldyn);
int moldyn_bc_check(t_moldyn *moldyn);
int get_line(int fd,char *line,int max);
-int calc_fluctuations(double start,double end,t_moldyn *moldyn);
-int get_heat_capacity(t_moldyn *moldyn);
#endif