X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=0dbc1f96a91981ef7908297568279f948d497fb7;hb=c0ddf2bdd8067456f39f6b63fe2261624ebde6b7;hp=23b510007a91f4fa3fc65911c6d938b670eea442;hpb=115ab83cedba54af2d165b8900781b98c5326b55;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index 23b5100..0dbc1f9 100644 --- a/moldyn.h +++ b/moldyn.h @@ -12,7 +12,6 @@ #include "random/random.h" #include "list/list.h" - /* * * datatypes @@ -71,7 +70,7 @@ typedef struct s_moldyn_schedule { int total_sched; int *runs; double *tau; - int (*hook)(void *moldyn,void *hook); + int (*hook)(void *moldyn,void *hook_params); void *hook_params; } t_moldyn_schedule; @@ -104,7 +103,9 @@ typedef struct s_moldyn { double t; /* actual temperature */ double p_ref; /* reference pressure */ - double p; /* actual pressure */ + double p; /* actual pressure (computed by virial) */ + t_3dvec tp; /* thermodynamic pressure dU/dV */ + double dv; /* dV for thermodynamic pressure calc */ /* pressure and temperature control (velocity/volume scaling) */ /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */ @@ -136,12 +137,16 @@ typedef struct s_moldyn { int mfd; /* fd for momentum log */ unsigned int vwrite; /* how often to visualize atom information */ unsigned int swrite; /* how often to create a save file */ + int rfd; /* report file descriptor */ + char rtitle[64]; /* report title */ + char rauthor[64]; /* report author */ + int pfd; /* gnuplot script file descriptor */ u8 status; /* general moldyn properties */ t_random random; /* random interface */ - int debug; /* debugging stuff, ignore */ + double debug; /* debugging stuff, ignore */ } t_moldyn; #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */ @@ -159,7 +164,6 @@ typedef struct s_moldyn { #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */ #define P_SCALE_DIRECT 0x08 /* direct p control */ - /* * * potential parameter structures @@ -183,6 +187,7 @@ typedef struct s_lj_params { double sigma6; double sigma12; double epsilon4; + double uc; } t_lj_params; /* @@ -230,7 +235,7 @@ typedef struct s_tersoff_exchange { t_3dvec dzeta_ji; } t_tersoff_exchange; -/* tersoff multi (2!) potential parameters */ +/* tersoff mult (2!) potential parameters */ typedef struct s_tersoff_mult_params { double S[2]; /* tersoff cutoff radii */ double S2[2]; /* tersoff cutoff radii squared */ @@ -285,7 +290,7 @@ typedef struct s_tersoff_mult_params { #define KILOGRAM (1.0/AMU) /* amu */ #define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */ #define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */ -#define ATM (1.0133e5*PASCAL) /* N / A^2 */ +#define ATM ((1.0133e5*PASCAL)) /* N / A^2 */ #define MOLDYN_TEMP 273.0 #define MOLDYN_TAU 1.0 @@ -303,6 +308,7 @@ typedef struct s_tersoff_mult_params { #define LOG_TOTAL_MOMENTUM 0x02 #define SAVE_STEP 0x04 #define VISUAL_STEP 0x08 +#define CREATE_REPORT 0x10 #define TRUE 1 #define FALSE 0 @@ -324,7 +330,8 @@ typedef struct s_tersoff_mult_params { #define LC_SI (0.543105e-9*METER) /* A */ #define M_SI 28.08553 /* amu */ -#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */ +//#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */ +#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */ #define LJ_EPSILON_SI (2.1678*EV) /* NA */ #define TM_R_SI (2.7e-10*METER) /* A */ @@ -357,8 +364,9 @@ typedef struct s_tersoff_mult_params { * lattice constants */ -#define FCC 0x01 -#define DIAMOND 0x02 +#define CUBIC 0x01 +#define FCC 0x02 +#define DIAMOND 0x04 /* @@ -389,11 +397,13 @@ int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params); int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params); 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 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); +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, @@ -401,11 +411,18 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr, 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 pressure_calc(t_moldyn *moldyn); +double thermodynamic_pressure_calc(t_moldyn *moldyn); +double get_pressure(t_moldyn *moldyn); int scale_volume(t_moldyn *moldyn); +int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z); +int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z); double get_e_kin(t_moldyn *moldyn); -double get_e_pot(t_moldyn *moldyn); +double update_e_kin(t_moldyn *moldyn); double get_total_energy(t_moldyn *moldyn); t_3dvec get_total_p(t_moldyn *moldyn); @@ -416,16 +433,19 @@ int link_cell_update(t_moldyn *moldyn); int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell); int link_cell_shutdown(t_moldyn *moldyn); +typedef int (*set_hook)(void *,void *); + int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau); -int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params); +int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params); int moldyn_integrate(t_moldyn *moldyn); int velocity_verlet(t_moldyn *moldyn); int potential_force_calc(t_moldyn *moldyn); +inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) + __attribute__((always_inline)); inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) __attribute__((always_inline)); -int check_per_bound(t_moldyn *moldyn,t_3dvec *a); int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); int tersoff_mult_complete_params(t_tersoff_mult_params *p);