X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.h;h=0670f3d19239ada190d6c7d65fd99317392af295;hp=de6157c10decf7e8bedb6937488511b41394276b;hb=HEAD;hpb=4c2140b0f76fb191bdd9b9c2a329877eb0aae531 diff --git a/moldyn.h b/moldyn.h index de6157c..0670f3d 100644 --- a/moldyn.h +++ b/moldyn.h @@ -45,16 +45,25 @@ typedef struct s_atom { u8 brand; /* brand id */ int tag; /* atom unique id (number of atom) */ u8 attr; /* attributes */ + int pbc[3]; /* pb crossing in x, y and z direction */ } 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_VA 0x04 /* visualize this atom */ +#define ATOM_ATTR_VA 0x04 /* visualize this atom */ // TODO #define ATOM_ATTR_VB 0x08 /* visualize the bond of this atom */ -#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 */ + +#define DEFAULT_ATOM_ATTR 0x74 // 1,2,3 body interaction + visualize + +/* special list structure for low mem approach */ +typedef struct s_lowmem_list { + int *head; + int *list; +} t_lowmem_list; /* cell lists */ typedef struct s_linkcell { @@ -64,6 +73,8 @@ typedef struct s_linkcell { double x,y,z; /* the actual cell lengthes */ #ifdef STATIC_LISTS int **subcell; /* pointer to the cell lists */ +#elif LOWMEM_LISTS + t_lowmem_list *subcell; /* low mem approach list */ #else t_list *subcell; /* pointer to the cell lists */ #endif @@ -102,22 +113,24 @@ typedef struct s_moldyn { 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); - int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); - int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); - int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); - int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); - int (*func3b_k1)(struct s_moldyn *moldyn, - t_atom *ai,t_atom *aj,t_atom *ak,u8 bck); - int (*func3b_k2)(struct s_moldyn *moldyn, - t_atom *ai,t_atom *aj,t_atom *ak,u8 bck); + int (*func_i0)(struct s_moldyn *moldyn,t_atom *ai); + int (*func_j0)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); + int (*func_j0_k0)(struct s_moldyn *moldyn, + t_atom *ai,t_atom *aj,t_atom *ak,u8 bck); + int (*func_j0e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); + int (*func_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); + int (*func_j1_k0)(struct s_moldyn *moldyn, + t_atom *ai,t_atom *aj,t_atom *ak,u8 bck); + int (*func_j1c)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); + int (*func_j1_k1)(struct s_moldyn *moldyn, + t_atom *ai,t_atom *aj,t_atom *ak,u8 bck); + int (*func_j1e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); void *pot_params; unsigned char run3bp; double cutoff; /* cutoff radius */ double cutoff_square; /* square of the cutoff radius */ double nnd; /* nearest neighbour distance (optional) */ - double bondlen[3]; /* bond lengthes (only 2 atomic systems) */ t_linkcell lc; /* linked cell list interface */ @@ -128,14 +141,22 @@ typedef struct s_moldyn { double t_sum; /* sum over all t */ double t_avg; /* average value of t */ + /* for sale! */ t_virial gvir; /* global virial (absolute coordinates) */ - double gv; - double gv_sum; - double gv_avg; - - double gp; /* pressure computed from global virial */ - double gp_sum; /* sum over all gp */ - double gp_avg; /* average value of gp */ + //double gv; + //double gv_sum; + //double gv_avg; + double sale1; + double sale2; + double sale3; + + // gp stuff exchanged by kinetic energies + //double gp; /* pressure computed from global virial */ + //double gp_sum; /* sum over all gp */ + //double gp_avg; /* average value of gp */ + double ekinx; + double ekiny; + double ekinz; t_virial vir; /* actual virial */ double virial; @@ -144,6 +165,7 @@ typedef struct s_moldyn { double p_ref; /* reference pressure */ double p; /* actual pressure (computed by virial) */ + double px,py,pz; /* components of pressure */ double p_sum; /* sum over all p */ double p_avg; /* average value of p */ @@ -236,6 +258,47 @@ typedef struct s_ba { int tcnt; } t_ba; +typedef struct s_vb { + int fd; +} t_vb; + +typedef struct s_part_params { + u8 type; + double r; + t_3dvec p; + t_3dvec d; +} t_part_params; + +#define PART_INSIDE_R 1 +#define PART_OUTSIDE_R 2 +#define PART_INSIDE_D 3 +#define PART_OUTSIDE_D 4 + +typedef struct s_defect_params { + u8 type; + u8 stype; + double od; + double dd; + int element; + u8 brand; + u8 attr; +} t_defect_params; + +#define DEFECT_TYPE_0D 1 +#define DEFECT_TYPE_1D 2 +#define DEFECT_TYPE_2D 3 +#define DEFECT_TYPE_3D 4 + +#define DEFECT_STYPE_DB_X 1 +#define DEFECT_STYPE_DB_Y 2 +#define DEFECT_STYPE_DB_Z 3 +#define DEFECT_STYPE_DB_R 4 + +typedef struct s_offset_params { + t_3dvec o; + u8 use; +} t_offset_params; + /* * * defines @@ -252,10 +315,15 @@ typedef struct s_ba { #define MOLDYN_2BP 0x20 /* 2 body */ #define MOLDYN_3BP 0x40 /* and 3 body particle pots */ +#define T_SCALE_NONE 0x00 #define T_SCALE_BERENDSEN 0x01 /* berendsen t control */ #define T_SCALE_DIRECT 0x02 /* direct t control */ +#define T_SCALE_MASK 0x03 + +#define P_SCALE_NONE 0x00 #define P_SCALE_BERENDSEN 0x04 /* berendsen p control */ #define P_SCALE_DIRECT 0x08 /* direct p control */ +#define P_SCALE_MASK 0x0c /* * default values & units @@ -293,6 +361,7 @@ typedef struct s_ba { #define MOLDYN_POTENTIAL_LJ 0x01 #define MOLDYN_POTENTIAL_TM 0x02 #define MOLDYN_POTENTIAL_AM 0x03 +#define MOLDYN_POTENTIAL_AO 0x04 #define LOG_TOTAL_ENERGY 0x01 #define LOG_TOTAL_MOMENTUM 0x02 @@ -314,12 +383,15 @@ typedef struct s_ba { #define SCALE_DIRECT 'D' /* - * potential related phsical values / constants - * + * usefull constants */ #define ONE_THIRD (1.0/3.0) +/* + * element specific defines + */ + #define C 0x06 #define LC_C 3.567 /* A */ #define M_C 12.011 /* amu */ @@ -330,11 +402,6 @@ typedef struct s_ba { #define LC_3C_SIC 4.3596 /* A */ -#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 */ - /* * lattice types */ @@ -342,6 +409,14 @@ typedef struct s_ba { #define CUBIC 0x01 #define FCC 0x02 #define DIAMOND 0x04 +#define ZINCBLENDE 0x08 +#define NONE 0x80 + +/* + * more includes + */ + +//#include "pse.h" /* * @@ -354,9 +429,10 @@ 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_bondlen(t_moldyn *moldyn,double b0,double b1,double bm); int set_temperature(t_moldyn *moldyn,double t_ref); int set_pressure(t_moldyn *moldyn,double p_ref); +int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc); +int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc); 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); @@ -370,14 +446,19 @@ 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,t_3dvec *origin); -int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr, +int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element, + u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin, + t_part_params *p_params,t_defect_params *d_params, + t_offset_params *o_params); +int add_atom(t_moldyn *moldyn,int element,u8 brand,u8 attr, t_3dvec *r,t_3dvec *v); int del_atom(t_moldyn *moldyn,int tag); -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 cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin, + t_part_params *p_params,t_defect_params *d_params); +int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin, + t_part_params *p_params,t_defect_params *d_params); +int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin, + t_part_params *p_params,t_defect_params *d_params); int destroy_atoms(t_moldyn *moldyn); int thermal_init(t_moldyn *moldyn,u8 equi_init); @@ -406,6 +487,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol); int link_cell_update(t_moldyn *moldyn); #ifdef STATIC_LISTS int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell); +#elif LOWMEM_LISTS +int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int *cell); #else int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell); #endif @@ -424,6 +507,7 @@ 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); +int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a); //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) // __attribute__((always_inline)); @@ -435,10 +519,15 @@ int moldyn_load(t_moldyn *moldyn); int process_2b_bonds(t_moldyn *moldyn,void *data, int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, void *data,u8 bc)); +int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom, + int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom, + void *data,u8 bc)); + int get_line(int fd,char *line,int max); int pair_correlation_init(t_moldyn *moldyn,double dr); int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc); +int calculate_msd(t_moldyn *moldyn,double *msd); int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom, t_atom *jtom,void *data,u8 bc); int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr); @@ -447,7 +536,15 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, int bond_analyze(t_moldyn *moldyn,double *quality); int visual_init(t_moldyn *moldyn,char *filebase); +int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, + void *data,u8 bc); +#ifdef VISUAL_THREAD +void *visual_atoms(void *ptr); +#else int visual_atoms(t_moldyn *moldyn); +#endif + +int fpu_set_rtd(void); #endif