X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=36e701ea0877d88118d4d6441d963b5c1cbac803;hb=684bf7c398cdfa98549b0c7a1fa37e6dc5b35bea;hp=868db6267784faa8d684d265e6a976668776f10f;hpb=25c22fe95e80365056c6a7fadc548119360ca8ce;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index 868db62..36e701e 100644 --- a/moldyn.h +++ b/moldyn.h @@ -33,11 +33,13 @@ typedef struct s_virial { /* 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 */ @@ -76,6 +78,9 @@ typedef struct s_moldyn_schedule { /* 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 */ @@ -102,25 +107,31 @@ typedef struct s_moldyn { t_linkcell lc; /* linked cell list interface */ - int mean_skip; /* amount of steps without average calc */ + 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 */ @@ -149,14 +160,14 @@ typedef struct s_moldyn { /* energy averages & fluctuations */ double k_sum; /* sum of kinetic energy */ double v_sum; /* sum of potential energy */ - double k_mean; /* average of kinetic energy */ - double v_mean; /* average 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_mean; /* average of kinetic energy squared */ - double v2_mean; /* average of potential energy squared */ - double dk2_mean; /* mean square kinetic energy fluctuations */ - double dv2_mean; /* mean square potential energy fluctuations */ + 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) */ @@ -316,7 +327,7 @@ typedef struct s_moldyn { #define ALBE_R_SI (2.82-0.14) #define ALBE_S_SI (2.82+0.14) #define ALBE_A_SI (3.24*EV/0.842) -#define ALBE_B_SI (1.842*3.24*EV/0.842) +#define ALBE_B_SI (-1.842*3.24*EV/0.842) #define ALBE_R0_SI 2.232 #define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842)) #define ALBE_MU_SI (1.4761*sqrt(2.0/1.842)) @@ -330,7 +341,7 @@ typedef struct s_moldyn { #define ALBE_R_C (2.00-0.15) #define ALBE_S_C (2.00+0.15) #define ALBE_A_C (6.00*EV/1.167) -#define ALBE_B_C (2.167*6.00*EV/1.167) +#define ALBE_B_C (-2.167*6.00*EV/1.167) #define ALBE_R0_C 1.4276 #define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167)) #define ALBE_MU_C (2.0099*sqrt(2.0/2.167)) @@ -342,9 +353,9 @@ typedef struct s_moldyn { #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_B_SIC (-1.847*4.36*EV/0.847) #define ALBE_R0_SIC 1.79 #define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847)) #define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847)) @@ -395,7 +406,7 @@ int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func); int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func); int set_potential_params(t_moldyn *moldyn,void *params); -int set_mean_skip(t_moldyn *moldyn,int skip); +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); @@ -404,11 +415,11 @@ int moldyn_log_shutdown(t_moldyn *moldyn); 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); @@ -416,6 +427,7 @@ 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);