X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.h;h=a76b3b4f804c9ad83bad01ab0b445b65066b5b1d;hb=d3d65b8212c02f787a16cb312bf08b7712e89550;hp=c6712ba41d1508fb8e359b627c71082e1307567a;hpb=0d71b08d4382b23b8217342caf138cfce36226cc;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index c6712ba..a76b3b4 100644 --- a/moldyn.h +++ b/moldyn.h @@ -13,25 +13,34 @@ #include "list/list.h" -/* datatypes */ +/* + * + * datatypes + * + */ +/* general */ +typedef unsigned char u8; /* the atom of the md simulation */ - typedef struct s_atom { t_3dvec r; /* position */ t_3dvec v; /* velocity */ t_3dvec f; /* force */ int element; /* number of element in pse */ double mass; /* atom mass */ - unsigned char attr; /* attributes */ + 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) */ -/* cell lists */ +#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; /* amount of cells in x, y and z direction */ int cells; /* total amount of cells */ @@ -39,109 +48,199 @@ 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" -# moldyn properties structure */ +# moldyn schedule structure */ +typedef struct s_moldyn_schedule { + int content_count; + int *runs; + int *tau; + int (*hook)(t_moldyn *,void *); + void *hook_params; +} t_moldyn_schedule; +/* moldyn main structure */ typedef struct s_moldyn { - int count; /* total amount of atoms */ t_atom *atom; /* pointer to the atoms */ + t_3dvec dim; /* dimensions of the simulation volume */ - /* potential, force & parameters */ - - /* potential force funtion created by the user */ - int (*potential_force_function)(struct s_moldyn *moldyn); - void *pot_params; /* parameters describing the potential */ - - double cutoff; - double cutoff_square; - /* linked list / cell method */ - t_linkcell lc; - /* temperature */ - double t; - /* integration of newtons equations */ + + /* potential force function and parameter pointers */ + int (*pf_func1b)(struct s_moldyn *,t_atom *); + void *pot1b_params; + int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *); + void *pot2b_params; + int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *); + void *pot3b_params; + //int (*potential_force_function)(struct s_moldyn *moldyn); + + double cutoff; /* cutoff radius */ + double cutoff_square; /* square of the cutoff radius */ + + t_linkcell lc; /* linked cell method */ + + double t; /* temperature */ + + /* 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 */ - t_visual vis; - 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; - /* random */ - t_random random; + int time_steps; /* amount of iterations */ + double tau; /* delta t */ + double tau_square; /* delta t squared */ + double elapsed; /* total elapsed time */ + + double energy; /* energy */ + + t_visual vis; /* visualization/log/save interface structure */ + u8 lvstat; /* log & vis properties */ + unsigned int ewrite; /* how often to log energy */ + char efb[64]; /* energy log filename */ + int efd; /* fd for energy log */ + unsigned int mwrite; /* how often to log momentum */ + char mfb[64]; /* momentum log filename */ + 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 */ + + u8 status; /* general moldyn properties */ + + t_random random; /* random interface */ } 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 0x08 /* periodic boudaries in x */ +#define MOLDYN_STAT_PBY 0x10 /* y */ +#define MOLDYN_STAT_PBZ 0x20 /* and z direction */ + + +/* + * + * 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; } t_lj_params; -typedef struct s_tersoff_params { - double l_1,l_2; - double m_1,m_2; - double a_1,a_2; - double b_1,b_2; - double r_1,r_2; - double s_1,s_2; +/* + * tersoff + */ + +/* tersoff exchange structure to exchange 2bp and 3bp calculated values */ +typedef struct s_tersoff_exchange { + double f_c,df_c; + + 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; + + u8 run3bp; +} 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_params; + + /* + * * defines + * */ -/* general defines */ - -#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 - -#define MOLDYN_STAT_POTENTIAL 0x01 -#define MOLDYN_STAT_FORCE 0x02 +/* default values */ #define MOLDYN_TEMP 273.0 #define MOLDYN_TAU 1.0e-15 -#define MOLDYN_CUTOFF 10.0e-9 +#define MOLDYN_CUTOFF 1.0e-9 #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 MOLDYN_SET_POTENTIAL 0x00 +#define MOLDYN_SET_TEMPERATURE 0x01 +#define MOLDYN_SET_ +#define MOLDYN_SET_ + +/* + * + * phsical values / constants + * + */ #define K_BOLTZMANN 1.3807e-27 /* Nm/K */ #define AMU 1.660540e-27 /* kg */ @@ -158,7 +257,12 @@ typedef struct s_tersoff_params { #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */ #define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */ -/* function prototypes */ + +/* + * + * function prototypes + * + */ int moldyn_usage(char **argv); int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv); @@ -166,7 +270,7 @@ int moldyn_log_init(t_moldyn *moldyn); 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 create_lattice(u8 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);