X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=85a4950cc513c9cde9b7dc0cb66f9d49503e3b8f;hb=ea612b88a0588b8f46fafaebf3b37fb46c83c0cf;hp=8254568af609f69d171862a7ba9d8023bee8decc;hpb=9f6af2cd82a72451741b68ca333f94c6c1d2eec5;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index 8254568..85a4950 100644 --- a/moldyn.h +++ b/moldyn.h @@ -12,7 +12,6 @@ #include "random/random.h" #include "list/list.h" - /* * * datatypes @@ -82,17 +81,14 @@ typedef struct s_moldyn { t_3dvec dim; /* dimensions of the simulation volume */ double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */ - double vt1,vt2; /* potential force function and parameter pointers */ int (*func1b)(struct s_moldyn *moldyn,t_atom *ai); - void *pot1b_params; int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); int (*func2b_post)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); - void *pot2b_params; int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak, u8 bck); - void *pot3b_params; + void *pot_params; //int (*potential_force_function)(struct s_moldyn *moldyn); double cutoff; /* cutoff radius */ @@ -105,7 +101,9 @@ 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.) */ @@ -135,16 +133,32 @@ typedef struct s_moldyn { int efd; /* fd for energy log */ unsigned int mwrite; /* how often to log momentum */ int mfd; /* fd for momentum log */ + unsigned int pwrite; /* how often to log pressure */ + int pfd; /* fd for pressure log */ + unsigned int twrite; /* how often to log temperature */ + int tfd; /* fd for temperature 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 epfd; /* energy gnuplot script file descriptor */ + int ppfd; /* pressure gnuplot script file descriptor */ + int tpfd; /* temperature 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; +/* + * + * defines + * + */ + #define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */ #define MOLDYN_STAT_PBY 0x02 /* y */ #define MOLDYN_STAT_PBZ 0x04 /* and z direction */ @@ -160,116 +174,6 @@ typedef struct s_moldyn { #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */ #define P_SCALE_DIRECT 0x08 /* direct p control */ - -/* - * - * potential parameter structures - * - */ - -/* - * harmonic oscillator potential parameter structure - */ - -typedef struct s_ho_params { - double spring_constant; - double equilibrium_distance; -} t_ho_params; - -/* - * lennard jones potential parameter structure - */ - -typedef struct s_lj_params { - double sigma6; - double sigma12; - double epsilon4; - double uc; -} t_lj_params; - -/* - * tersoff - */ - -/* tersoff exchange structure to exchange 2bp and 3bp calculated values */ -typedef struct s_tersoff_exchange { - double f_c,df_c; - double f_a,df_a; - - t_3dvec dist_ij; - double d_ij2; - double d_ij; - - double chi; - - double *beta_i; - double *beta_j; - double *n_i; - double *n_j; - double *c_i; - double *c_j; - double *d_i; - double *d_j; - double *h_i; - double *h_j; - - double ci2; - double cj2; - double di2; - double dj2; - double ci2di2; - double cj2dj2; - double betaini; - double betajnj; - - u8 run3bp; - u8 run2bp_post; - u8 d_ij_between_rs; - - double zeta_ij; - double zeta_ji; - t_3dvec dzeta_ij; - t_3dvec dzeta_ji; -} t_tersoff_exchange; - -/* tersoff multi (2!) potential parameters */ -typedef struct s_tersoff_mult_params { - double S[2]; /* tersoff cutoff radii */ - double S2[2]; /* tersoff cutoff radii squared */ - double R[2]; /* tersoff cutoff radii */ - double Smixed; /* mixed S radius */ - double S2mixed; /* mixed S radius squared */ - double Rmixed; /* mixed R radius */ - double A[2]; /* factor of tersoff attractive part */ - double B[2]; /* factor of tersoff repulsive part */ - double Amixed; /* mixed A factor */ - double Bmixed; /* mixed B factor */ - double lambda[2]; /* tersoff lambda */ - double lambda_m; /* mixed lambda */ - double mu[2]; /* tersoff mu */ - double mu_m; /* mixed mu */ - - double chi; - - double beta[2]; - double n[2]; - double c[2]; - double d[2]; - double h[2]; - - t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */ -} t_tersoff_mult_params; - - - -/* - * - * defines - * - */ - -#define ONE_THIRD (1.0/3.0) - /* * default values * @@ -287,7 +191,7 @@ 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 @@ -303,12 +207,18 @@ typedef struct s_tersoff_mult_params { #define LOG_TOTAL_ENERGY 0x01 #define LOG_TOTAL_MOMENTUM 0x02 -#define SAVE_STEP 0x04 -#define VISUAL_STEP 0x08 +#define LOG_PRESSURE 0x04 +#define LOG_TEMPERATURE 0x08 +#define SAVE_STEP 0x10 +#define VISUAL_STEP 0x20 +#define CREATE_REPORT 0x40 #define TRUE 1 #define FALSE 0 +#define VERBOSE 1 +#define QUIET 0 + /* * * phsical values / constants @@ -316,6 +226,8 @@ typedef struct s_tersoff_mult_params { * */ +#define ONE_THIRD (1.0/3.0) + #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */ #define EV (1.6021765314e-19*METER*NEWTON) /* NA */ @@ -327,6 +239,8 @@ typedef struct s_tersoff_mult_params { #define M_SI 28.08553 /* amu */ #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_SIGMA_SI (0.5*sqrt(2.0)*LC_SI/1.122462) /* A */ #define LJ_EPSILON_SI (2.1678*EV) /* NA */ #define TM_R_SI (2.7e-10*METER) /* A */ @@ -359,8 +273,9 @@ typedef struct s_tersoff_mult_params { * lattice constants */ -#define FCC 0x01 -#define DIAMOND 0x02 +#define CUBIC 0x01 +#define FCC 0x02 +#define DIAMOND 0x04 /* @@ -385,17 +300,20 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc); int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize); int set_nn_dist(t_moldyn *moldyn,double dist); int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z); -int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params); -int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params); -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 set_potential1b(t_moldyn *moldyn,pf_func1b func); +int set_potential2b(t_moldyn *moldyn,pf_func2b func); +int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func); +int set_potential3b(t_moldyn *moldyn,pf_func3b func); +int set_potential_params(t_moldyn *moldyn,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, @@ -407,8 +325,11 @@ 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 update_e_kin(t_moldyn *moldyn); @@ -417,7 +338,7 @@ t_3dvec get_total_p(t_moldyn *moldyn); double estimate_time_step(t_moldyn *moldyn,double nn_dist); -int link_cell_init(t_moldyn *moldyn); +int link_cell_init(t_moldyn *moldyn,u8 vol); 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); @@ -431,17 +352,12 @@ 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 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); -int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai); -int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); -int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); -int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc); +int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d); +//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) +// __attribute__((always_inline)); +int check_per_bound(t_moldyn *moldyn,t_3dvec *a); +//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) +// __attribute__((always_inline)); int moldyn_bc_check(t_moldyn *moldyn);