X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=2d4ca4873109a80732606ff7f425d764d8b59259;hb=95cfeec6fbbfa975d5ac5b99ec3f7386ca3d6071;hp=2d1a438b3935b05cc8dfd791a6505b8abf03a093;hpb=0fbd532d8ddce9848df592ed586ffba439369284;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index 2d1a438..2d4ca48 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 */ @@ -47,6 +49,8 @@ typedef struct s_atom { #define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */ #define ATOM_ATTR_HB 0x02 /* coupled to heat bath (velocity scaling) */ +#define ATOM_ATTR_VA 0x04 /* visualize this atom */ +#define ATOM_ATTR_VB 0x08 /* visualize the bond of this atom */ #define ATOM_ATTR_1BP 0x10 /* single paricle potential */ #define ATOM_ATTR_2BP 0x20 /* pair potential */ @@ -62,8 +66,6 @@ typedef struct s_linkcell { int dnlc; /* direct neighbour lists counter */ } t_linkcell; -#include "visual/visual.h" - /* moldyn schedule structure */ typedef struct s_moldyn_schedule { int count; @@ -74,8 +76,18 @@ typedef struct s_moldyn_schedule { void *hook_params; } t_moldyn_schedule; +/* visualization structure */ +typedef struct s_visual { + int fd; /* rasmol script file descriptor */ + char fb[128]; /* basename of the save files */ + t_3dvec dim; /* dimensions of the simulation cell */ +} t_visual; + /* 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 */ @@ -99,26 +111,35 @@ typedef struct s_moldyn { double cutoff; /* cutoff radius */ double cutoff_square; /* square of the cutoff radius */ double nnd; /* nearest neighbour distance (optional) */ + double bondlen[3]; /* bond lengthes (only 2 atomic systems) */ 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 */ @@ -147,14 +168,14 @@ 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) */ @@ -309,12 +330,12 @@ typedef struct s_moldyn { #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_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)) @@ -323,12 +344,12 @@ typedef struct s_moldyn { #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_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)) @@ -337,12 +358,12 @@ typedef struct s_moldyn { #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_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)) @@ -351,7 +372,7 @@ typedef struct s_moldyn { #define ALBE_D_SIC 180.314 #define ALBE_H_SIC 0.68 -#define LC_SIC_ALBE 4.359 +#define ALBE_LC_SIC 4.359 /* @@ -362,7 +383,6 @@ typedef struct s_moldyn { #define FCC 0x02 #define DIAMOND 0x04 - /* * * function prototypes @@ -378,6 +398,7 @@ int moldyn_shutdown(t_moldyn *moldyn); int set_int_alg(t_moldyn *moldyn,u8 algo); int set_cutoff(t_moldyn *moldyn,double cutoff); +int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm); int set_temperature(t_moldyn *moldyn,double t_ref); int set_pressure(t_moldyn *moldyn,double p_ref); int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc); @@ -393,6 +414,8 @@ 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_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); @@ -400,11 +423,12 @@ 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 del_atom(t_moldyn *moldyn,int tag); 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); @@ -412,6 +436,7 @@ 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); @@ -452,4 +477,8 @@ int moldyn_bc_check(t_moldyn *moldyn); int get_line(int fd,char *line,int max); +int visual_init(t_moldyn *moldyn,char *filebase); +int visual_atoms(t_moldyn *moldyn); + #endif +