X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.h;h=66f774eb068cd1b296d7f7277682a74b3bf461ba;hb=0656efc2936da55ecf0b818fe33bb2acebc689c6;hp=b43ed8eed5cffb1f0b6feaa8206a88bc45dfec5a;hpb=85abe46fecc79a3d7885ff6124186b2be2ca96ac;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index b43ed8e..66f774e 100644 --- a/moldyn.h +++ b/moldyn.h @@ -10,70 +10,188 @@ #include "math/math.h" #include "random/random.h" +#include "list/list.h" + /* datatypes */ +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 */ + int element; /* number of element in pse */ + double mass; /* atom mass */ + unsigned char 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; /* 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 */ + int countn; /* amount of neighbours */ +} t_linkcell; + +#include "visual/visual.h" + +# moldyn structure */ + typedef struct s_moldyn { - int count; - t_atom *atom; - double (*potential)(struct s_moldyn *moldyn); - void *pot_params; - int (*force)(struct s_moldyn *moldyn); - double cutoff_square; - t_3dvec dim; - unsigned char status; + + int count; /* total amount of atoms */ + t_atom *atom; /* pointer to the atoms */ + + t_3dvec dim; /* dimensions of the simulation volume */ + + /* potential force function pointer and parameters */ + int (*pf_func1b)(struct s_moldyn *,t_atom *); + int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *); + int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *); + //int (*potential_force_function)(struct s_moldyn *moldyn); + void *pot_params; /* parameters describing the potential */ + + double cutoff; /* cutoff radius */ + double cutoff_square; /* square of the cutoff radius */ + + t_linkcell lc; /* linked cell method */ + + double t; /* temperature */ + + /* integration function pointer */ + int (*integrate)(struct s_moldyn *moldyn); + int time_steps; /* amount of iterations */ + double tau; /* delta t */ + double tau_square; /* delta t squared */ + + double energy; /* energy */ + + t_visual vis; /* visualization/log/save interface structure */ + unsigned char 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 */ + + unsigned char 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 */ + +typedef struct s_ho_params { + double spring_constant; + double equilibrium_distance; +} t_ho_params; + typedef struct s_lj_params { double sigma6; double sigma12; - double epsilon; + 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; +} t_tersoff_params; + /* * defines */ /* general defines */ -#define MOLDYN_STAT_POTENTIAL 0x01 -#define MOLDYN_STAT_FORCE 0x02 +#define MOLDYN_TEMP 273.0 +#define MOLDYN_TAU 1.0e-15 +#define MOLDYN_CUTOFF 10.0e-9 +#define MOLDYN_RUNS 1000000 + +#define MOLDYN_INTEGRATE_VERLET 0x00 +#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET + +#define MOLDYN_POTENTIAL_HO 0x00 +#define MOLDYN_POTENTIAL_LJ 0x01 +#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ /* phsical values */ -//#define K_BOLTZMANN 1.3807E-23 -#define K_BOLTZMANN 1.0 +#define K_BOLTZMANN 1.3807e-27 /* Nm/K */ +#define AMU 1.660540e-27 /* kg */ #define FCC 0x01 #define DIAMOND 0x02 #define C 0x06 -#define M_C 6.0 +#define M_C (12.011*AMU) -#define Si 0x0e -#define M_SI 14.0 -#define LC_SI 5.43105 +#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 */ /* function prototypes */ +int moldyn_usage(char **argv); +int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv); +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 a,int b,int c,t_atom **atom); int destroy_lattice(t_atom *atom); -int thermal_init(t_atom *atom,t_random *random,int count,double t); -int scale_velocity(t_atom *atom,int count,double t); +int thermal_init(t_moldyn *moldyn); +int scale_velocity(t_moldyn *moldyn); double get_e_kin(t_atom *atom,int count); double get_e_pot(t_moldyn *moldyn); double get_total_energy(t_moldyn *moldyn); t_3dvec get_total_p(t_atom *atom,int count); -double potential_lennard_jones(t_moldyn *moldyn); +double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t); + +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_integrate(t_moldyn *moldyn); +int velocity_verlet(t_moldyn *moldyn); + +int harmonic_oscillator(t_moldyn *moldyn); +int lennard_jones(t_moldyn *moldyn); #endif