X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=c01bc9f6e5e81da8cca4ca56c8206ea21e4aed81;hb=785f05e0c0ddb57428dc71b0a3f7798673799871;hp=e9f1495355df4dad8a44f3779f678649b328a99d;hpb=e6f456c0fa807b86e1b25996e70efcdcfe390ea5;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index e9f1495..c01bc9f 100644 --- a/moldyn.h +++ b/moldyn.h @@ -12,72 +12,160 @@ #include "random/random.h" #include "list/list.h" -/* datatypes */ +/* + * + * datatypes + * + */ + +/* general */ +typedef unsigned char u8; + +/* the atom of the md simulation */ typedef struct s_atom { - t_3dvec r; /* positions */ - t_3dvec v; /* velocities */ - t_3dvec f; /* forces */ - int element; /* number of element in pse */ - double mass; /* atom mass */ + 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 */ + u8 attr; /* attributes */ } t_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 */ + +/* cell lists */ typedef struct s_linkcell { - int nx,ny,nz; - double x,y,z; - t_list *subcell; + int nx,ny,nz; /* amount of cells in x, y and z direction */ + int cells; /* total amount of cells */ + double len; /* prefered cell edge length */ + double x,y,z; /* the actual cell lengthes */ + t_list *subcell; /* pointer to the cell lists */ + int dnlc; /* direct neighbour lists counter */ } t_linkcell; #include "visual/visual.h" +/* moldyn schedule structure */ +typedef struct s_moldyn_schedule { + int content_count; + int *runs; + double *tau; + int (*hook)(void *moldyn,void *hook); + void *hook_params; +} t_moldyn_schedule; + +/* moldyn main structure */ typedef struct s_moldyn { - /* atoms, amount, dimensions */ - int count; - t_atom *atom; - t_3dvec dim; - /* potential, force & parameters */ - int (*potential_force_function)(struct s_moldyn *moldyn); - void *pot_params; - /* cut off radius */ - double cutoff; - double cutoff_square; - /* linked list / cell method */ - t_linkcell lc; - /* temperature */ - double t; - /* integration of newtons equations */ + int count; /* total amount of atoms */ + 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 (*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; + //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 list interface */ + + 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; + int current; /* current position in schedule */ + + /* integration function pointer */ int (*integrate)(struct s_moldyn *moldyn); - int time_steps; - double tau; - double tau_square; - /* energy */ - double energy; - /* logging & visualization */ - unsigned char lvstat; - unsigned int ewrite; - char efb[64]; - int efd; - unsigned int mwrite; - char mfb[64]; - int mfd; - unsigned int swrite; - char sfb[64]; - int sfd; - unsigned int dwrite; - char dfb[64]; - int dfd; - unsigned int vwrite; - char vfb[64]; - void *visual; - /* moldyn general status */ - unsigned char status; + 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 */ + + 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 */ + unsigned int swrite; /* how often to create a save file */ + + u8 status; /* general moldyn properties */ + + t_random random; /* random interface */ + + int debug; /* debugging stuff, ignore */ } t_moldyn; +#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_1BP 0x10 /* care about single */ +#define MOLDYN_2BP 0x20 /* 2 body */ +#define MOLDYN_3BP 0x40 /* and 3 body particle pots */ + +#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 */ + + +/* + * + * 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; @@ -85,77 +173,250 @@ typedef struct s_lj_params { } 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_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 R[2]; /* tersoff cutoff radii */ + double Smixed; /* mixed S radius */ + 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 + * */ -/* general defines */ +#define ONE_THIRD (1.0/3.0) -#define MOLDYN_LVSTAT_TOTAL_E 0x01 -#define MOLDYN_LVSTAT_TOTAL_M 0x02 -#define MOLDYN_LVSTAT_SAVE 0x04 -#define MOLDYN_LVSTAT_DUMP 0x08 -#define MOLDYN_LVSTAT_VISUAL 0x10 -#define MOLDYN_LVSTAT_INITIALIZED 0x80 +/* + * 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 MOLDYN_STAT_POTENTIAL 0x01 -#define MOLDYN_STAT_FORCE 0x02 +#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_TAU 1.0 +#define MOLDYN_CUTOFF 10.0 #define MOLDYN_RUNS 1000000 #define MOLDYN_INTEGRATE_VERLET 0x00 -#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET +#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET #define MOLDYN_POTENTIAL_HO 0x00 #define MOLDYN_POTENTIAL_LJ 0x01 -#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ +#define MOLDYN_POTENTIAL_TM 0x02 -/* phsical values */ +#define LOG_TOTAL_ENERGY 0x01 +#define LOG_TOTAL_MOMENTUM 0x02 +#define SAVE_STEP 0x04 +#define VISUAL_STEP 0x08 -#define K_BOLTZMANN 1.3807e-27 /* Nm/K */ -#define AMU 1.660540e-27 /* kg */ +#define TRUE 1 +#define FALSE 0 -#define FCC 0x01 -#define DIAMOND 0x02 +/* + * + * phsical values / constants + * + * + */ + +#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 + -/* function prototypes */ +/* + * + * function prototypes + * + */ + +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_usage(char **argv); -int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv); -int moldyn_log_init(t_moldyn *moldyn,void *v); +int moldyn_init(t_moldyn *moldyn,int argc,char **argv); int moldyn_shutdown(t_moldyn *moldyn); -int create_lattice(unsigned char type,int element,double mass,double lc, - int a,int b,int c,t_atom **atom); -int destroy_lattice(t_atom *atom); -int thermal_init(t_moldyn *moldyn,t_random *random); -int scale_velocity(t_moldyn *moldyn); -double get_e_kin(t_atom *atom,int count); +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_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_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_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); +int destroy_atoms(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_atom *atom,int count); +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); int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell); int link_cell_shutdown(t_moldyn *moldyn); +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_integrate(t_moldyn *moldyn); int velocity_verlet(t_moldyn *moldyn); -int harmonic_oscillator(t_moldyn *moldyn); -int lennard_jones(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 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