X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=c01bc9f6e5e81da8cca4ca56c8206ea21e4aed81;hb=785f05e0c0ddb57428dc71b0a3f7798673799871;hp=dafd86cb67d415636833bafc147d860dd595850f;hpb=11bf064825efc474fa93c7270870856769a63e84;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index dafd86c..c01bc9f 100644 --- a/moldyn.h +++ b/moldyn.h @@ -27,6 +27,7 @@ typedef struct s_atom { t_3dvec r; /* position */ t_3dvec v; /* velocity */ t_3dvec f; /* force */ + t_3dvec virial; /* virial */ int element; /* number of element in pse */ double mass; /* atom mass */ u8 bnum; /* brand number */ @@ -36,9 +37,9 @@ 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_1BP 0x10 /* single paricle potential */ -#define ATOM_ATTR_2BP 0x20 /* pair potential */ -#define ATOM_ATTR_3BP 0x40 /* 3 body potential */ +#define ATOM_ATTR_1BP 0x10 /* single paricle potential */ +#define ATOM_ATTR_2BP 0x20 /* pair potential */ +#define ATOM_ATTR_3BP 0x40 /* 3 body potential */ /* cell lists */ typedef struct s_linkcell { @@ -48,7 +49,6 @@ typedef struct s_linkcell { double x,y,z; /* the actual cell lengthes */ t_list *subcell; /* pointer to the cell lists */ int dnlc; /* direct neighbour lists counter */ - int countn; /* amount of neighbours */ } t_linkcell; #include "visual/visual.h" @@ -68,22 +68,36 @@ typedef struct s_moldyn { t_atom *atom; /* pointer to the atoms */ t_3dvec dim; /* dimensions of the simulation volume */ + double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */ /* potential force function and parameter pointers */ - int (*pf_func1b)(struct s_moldyn *,t_atom *); + int (*func1b)(struct s_moldyn *moldyn,t_atom *ai); void *pot1b_params; - int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *); + 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 (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *); + int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak, + u8 bck); void *pot3b_params; //int (*potential_force_function)(struct s_moldyn *moldyn); double cutoff; /* cutoff radius */ double cutoff_square; /* square of the cutoff radius */ + double nnd; /* nearest neighbour distance (optional) */ - t_linkcell lc; /* linked cell method */ + t_linkcell lc; /* linked cell list interface */ - double t; /* temperature */ + double t_ref; /* reference temperature */ + double t; /* actual temperature */ + + double p_ref; /* reference pressure */ + double p; /* actual pressure */ + + /* pressure and temperature control (velocity/volume scaling) */ + /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */ + unsigned char pt_scale; /* type of p and t scaling */ + double t_tc; /* t berendsen control time constant */ + double p_tc; /* p berendsen control time constant */ /* simulation schedule */ t_moldyn_schedule schedule; @@ -93,42 +107,44 @@ typedef struct s_moldyn { int (*integrate)(struct s_moldyn *moldyn); int time_steps; /* amount of iterations */ double tau; /* delta t */ + double time; /* absolute time */ double tau_square; /* delta t squared */ double elapsed; /* total elapsed time */ double energy; /* potential energy */ double ekin; /* kinetic energy */ - t_visual vis; /* visualization/log/save interface structure */ - u8 lvstat; /* log & vis properties */ + char vlsdir[128]; /* visualization/log/save directory */ + t_visual vis; /* visualization interface structure */ + u8 vlsprop; /* log/vis/save properties */ unsigned int ewrite; /* how often to log energy */ int efd; /* fd for energy log */ unsigned int mwrite; /* how often to log momentum */ int mfd; /* fd for momentum log */ unsigned int vwrite; /* how often to visualize atom information */ - char vfb[64]; /* visualization file name base */ - void *visual; /* pointer (hack!) */ unsigned int swrite; /* how often to create a save file */ - char sfb[64]; /* visualization file name base */ u8 status; /* general moldyn properties */ t_random random; /* random interface */ + + int debug; /* debugging stuff, ignore */ } t_moldyn; -#define MOLDYN_LVSTAT_TOTAL_E 0x01 -#define MOLDYN_LVSTAT_TOTAL_M 0x02 -#define MOLDYN_LVSTAT_SAVE 0x04 -#define MOLDYN_LVSTAT_VISUAL 0x08 -#define MOLDYN_LVSTAT_INITIALIZED 0x10 +#define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */ +#define MOLDYN_STAT_PBY 0x02 /* y */ +#define MOLDYN_STAT_PBZ 0x04 /* and z direction */ + +#define MOLDYN_PSCALE 0x08 /* size controlled by piston */ -#define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */ -#define MOLDYN_STAT_PBY 0x10 /* y */ -#define MOLDYN_STAT_PBZ 0x20 /* and z direction */ +#define MOLDYN_1BP 0x10 /* care about single */ +#define MOLDYN_2BP 0x20 /* 2 body */ +#define MOLDYN_3BP 0x40 /* and 3 body particle pots */ -#define MOLDYN_1BP 0x00 -#define MOLDYN_2BP 0x01 -#define MOLDYN_3BP 0x02 +#define T_SCALE_BERENDSEN 0x01 /* berendsen t control */ +#define T_SCALE_DIRECT 0x02 /* direct t control */ +#define P_SCALE_BERENDSEN 0x04 /* berendsen p control */ +#define P_SCALE_DIRECT 0x08 /* direct p control */ /* @@ -163,28 +179,41 @@ typedef struct s_lj_params { /* 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_ij; - double d_ij2; double chi; - double *B; - double *mu; - - double *beta; - double *n; - double *c; - double *d; - double *h; - - double c2; - double d2; - double c2d2; - double betan; + 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 */ @@ -211,7 +240,7 @@ typedef struct s_tersoff_mult_params { double h[2]; t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */ -} t_tersoff_params; +} t_tersoff_mult_params; @@ -221,11 +250,30 @@ typedef struct s_tersoff_mult_params { * */ -/* default values */ +#define ONE_THIRD (1.0/3.0) + +/* + * default values + * + * - length unit: 1 A (1 A = 1e-10 m) + * - time unit: 1 fs (1 fs = 1e-15 s) + * - mass unit: 1 amu (1 amu = 1.6605388628e-27 kg ) + * + * fyi: in the following 1 N = (amu*A)/(fs*fs) + * + */ + +#define METER 1e10 /* A */ +#define SECOND 1e15 /* fs */ +#define AMU 1.6605388628e-27 /* kg */ +#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 MOLDYN_TEMP 273.0 -#define MOLDYN_TAU 1.0e-15 -#define MOLDYN_CUTOFF 1.0e-9 +#define MOLDYN_TAU 1.0 +#define MOLDYN_CUTOFF 10.0 #define MOLDYN_RUNS 1000000 #define MOLDYN_INTEGRATE_VERLET 0x00 @@ -235,10 +283,10 @@ typedef struct s_tersoff_mult_params { #define MOLDYN_POTENTIAL_LJ 0x01 #define MOLDYN_POTENTIAL_TM 0x02 -#define MOLDYN_SET_POTENTIAL 0x00 -#define MOLDYN_SET_TEMPERATURE 0x01 -#define MOLDYN_SET_ -#define MOLDYN_SET_ +#define LOG_TOTAL_ENERGY 0x01 +#define LOG_TOTAL_MOMENTUM 0x02 +#define SAVE_STEP 0x04 +#define VISUAL_STEP 0x08 #define TRUE 1 #define FALSE 0 @@ -247,22 +295,53 @@ typedef struct s_tersoff_mult_params { * * phsical values / constants * + * */ -#define K_BOLTZMANN 1.3807e-27 /* Nm/K */ -#define AMU 1.660540e-27 /* kg */ - -#define FCC 0x01 -#define DIAMOND 0x02 +#define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */ +#define EV (1.6021765314e-19*METER*NEWTON) /* NA */ #define C 0x06 -#define M_C (12.011*AMU) +#define M_C 12.011 /* amu */ #define SI 0x0e -#define LC_SI 0.543105e-9 /* m */ -#define M_SI (28.085*AMU) /* kg */ -#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */ -#define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */ +#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_EPSILON_SI (2.1678*EV) /* NA */ + +#define TM_R_SI (2.7e-10*METER) /* A */ +#define TM_S_SI (3.0e-10*METER) /* A */ +#define TM_A_SI (1830.8*EV) /* NA */ +#define TM_B_SI (471.18*EV) /* NA */ +#define TM_LAMBDA_SI (2.4799e10/METER) /* 1/A */ +#define TM_MU_SI (1.7322e10/METER) /* 1/A */ +#define TM_BETA_SI 1.1000e-6 +#define TM_N_SI 0.78734 +#define TM_C_SI 1.0039e5 +#define TM_D_SI 16.217 +#define TM_H_SI -0.59825 + +#define TM_R_C (1.8e-10*METER) /* A */ +#define TM_S_C (2.1e-10*METER) /* A */ +#define TM_A_C (1393.6*EV) /* NA */ +#define TM_B_C (346.7*EV) /* NA */ +#define TM_LAMBDA_C (3.4879e10/METER) /* 1/A */ +#define TM_MU_C (2.2119e10/METER) /* 1/A */ +#define TM_BETA_C 1.5724e-7 +#define TM_N_C 0.72751 +#define TM_C_C 3.8049e4 +#define TM_D_C 4.384 +#define TM_H_C -0.57058 + +#define TM_CHI_SIC 0.9776 + +/* + * lattice constants + */ + +#define FCC 0x01 +#define DIAMOND 0x02 /* @@ -271,34 +350,49 @@ typedef struct s_tersoff_mult_params { * */ +typedef int (*pf_func1b)(t_moldyn *,t_atom *ai); +typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc); +typedef int (*pf_func2b_post)(t_moldyn *,t_atom *,t_atom *,u8 bc); +typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc); + int moldyn_init(t_moldyn *moldyn,int argc,char **argv); 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_temperature(t_moldyn *moldyn,double t); +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); 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_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params); +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 moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer); -nt moldyn_log_shutdown(t_moldyn *moldyn); +int moldyn_set_log_dir(t_moldyn *moldyn,char *dir); +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 bnum,int a,int b,int c); +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 bnum,u8 attr, - t_3dvec r,t_3dvec v); + t_3dvec *r,t_3dvec *v); int destroy_atoms(t_moldyn *moldyn); -int thermal_init(t_moldyn *moldyn); -int scale_velocity(t_moldyn *moldyn); +int thermal_init(t_moldyn *moldyn,u8 equi_init); +int scale_velocity(t_moldyn *moldyn,u8 equi_init); +int scale_volume(t_moldyn *moldyn); double get_e_kin(t_moldyn *moldyn); double get_e_pot(t_moldyn *moldyn); double get_total_energy(t_moldyn *moldyn); t_3dvec get_total_p(t_moldyn *moldyn); -double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t); +double estimate_time_step(t_moldyn *moldyn,double nn_dist); int link_cell_init(t_moldyn *moldyn); int link_cell_update(t_moldyn *moldyn); @@ -312,11 +406,17 @@ int moldyn_integrate(t_moldyn *moldyn); int velocity_verlet(t_moldyn *moldyn); int potential_force_calc(t_moldyn *moldyn); +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 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 moldyn_bc_check(t_moldyn *moldyn); + #endif