X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=1647c1c314cc71fd17cc57216ae3d732417dc676;hb=2346d076f3d0955fb3a7bfb47f2b17b9eae6dd5b;hp=36e701ea0877d88118d4d6441d963b5c1cbac803;hpb=684bf7c398cdfa98549b0c7a1fa37e6dc5b35bea;p=physik%2Fposic.git diff --git a/moldyn.h b/moldyn.h index 36e701e..1647c1c 100644 --- a/moldyn.h +++ b/moldyn.h @@ -49,6 +49,8 @@ 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_VA 0x04 /* visualize this atom */ +#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 */ @@ -60,11 +62,15 @@ typedef struct s_linkcell { int cells; /* total amount of cells */ double len; /* prefered cell edge length */ double x,y,z; /* the actual cell lengthes */ +#ifdef STATIC_LISTS + int **subcell; /* pointer to the cell lists */ +#else t_list *subcell; /* pointer to the cell lists */ +#endif int dnlc; /* direct neighbour lists counter */ } t_linkcell; -#include "visual/visual.h" +#define MAX_ATOMS_PER_LIST 20 /* moldyn schedule structure */ typedef struct s_moldyn_schedule { @@ -76,6 +82,13 @@ typedef struct s_moldyn_schedule { void *hook_params; } t_moldyn_schedule; +/* visualization structure */ +typedef struct s_visual { + int fd; /* rasmol script file descriptor */ + char fb[128]; /* basename of the save files */ + t_3dvec dim; /* dimensions of the simulation cell */ +} t_visual; + /* moldyn main structure */ typedef struct s_moldyn { int argc; /* number of arguments */ @@ -104,6 +117,7 @@ typedef struct s_moldyn { 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 */ @@ -123,7 +137,8 @@ typedef struct s_moldyn { double gp_sum; /* sum over all gp */ double gp_avg; /* average value of gp */ - double virial; /* actual virial */ + t_virial vir; /* actual virial */ + double virial; double virial_sum; /* sum over all calculated virials */ double virial_avg; /* average of virial */ @@ -132,8 +147,10 @@ typedef struct s_moldyn { double p_sum; /* sum over all p */ double p_avg; /* average value of p */ - t_3dvec tp; /* thermodynamic pressure dU/dV */ - double dv; /* dV for thermodynamic pressure calc */ + double tp; /* thermodynamic pressure dU/dV */ + double tp_sum; /* sum over dU/dV pressure */ + double tp_avg; /* average value of dU/dV pressure */ + int tp_cnt; /* how often to do thermodynamic p calc */ /* pressure and temperature control (velocity/volume scaling) */ /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */ @@ -184,7 +201,9 @@ typedef struct s_moldyn { int pfd; /* fd for pressure log */ unsigned int twrite; /* how often to log temperature */ int tfd; /* fd for temperature log */ - unsigned int vwrite; /* how often to visualize atom information */ + unsigned int vwrite; /* how often to log volume */ + int vfd; /* fd for volume log */ + unsigned int awrite; /* how often to visualize atom information */ unsigned int swrite; /* how often to create a save file */ int rfd; /* report file descriptor */ char rtitle[64]; /* report title */ @@ -200,6 +219,19 @@ typedef struct s_moldyn { double debug; /* debugging stuff, ignore */ } t_moldyn; +typedef struct s_pcc { + int o1; + int o2; + double dr; + double *stat; +} t_pcc; + +typedef struct s_ba { + int *acnt; + int *bcnt; + int tcnt; +} t_ba; + /* * * defines @@ -238,6 +270,7 @@ typedef struct s_moldyn { #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 GPA (1e9*PASCAL) /* N / A^2 */ #define BAR ((1.0e5*PASCAL)) /* N / A^2 */ #define K_BOLTZMANN (1.380650524e-23*METER*NEWTON) /* NA/K */ #define K_B2 (K_BOLTZMANN*K_BOLTZMANN) /* (NA)^2/K^2 */ @@ -260,9 +293,10 @@ typedef struct s_moldyn { #define LOG_TOTAL_MOMENTUM 0x02 #define LOG_PRESSURE 0x04 #define LOG_TEMPERATURE 0x08 -#define SAVE_STEP 0x10 -#define VISUAL_STEP 0x20 -#define CREATE_REPORT 0x40 +#define LOG_VOLUME 0x10 +#define SAVE_STEP 0x20 +#define VISUAL_STEP 0x40 +#define CREATE_REPORT 0x80 #define TRUE 1 #define FALSE 0 @@ -375,7 +409,6 @@ typedef struct s_moldyn { #define FCC 0x02 #define DIAMOND 0x04 - /* * * function prototypes @@ -391,6 +424,7 @@ 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_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc); @@ -417,6 +451,7 @@ 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, 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); @@ -429,7 +464,8 @@ double get_temperature(t_moldyn *moldyn); int scale_velocity(t_moldyn *moldyn,u8 equi_init); double virial_sum(t_moldyn *moldyn); double pressure_calc(t_moldyn *moldyn); -int energy_fluctuation_calc(t_moldyn *moldyn); +int average_reset(t_moldyn *moldyn); +int average_and_fluctuation_calc(t_moldyn *moldyn); int get_heat_capacity(t_moldyn *moldyn); double thermodynamic_pressure_calc(t_moldyn *moldyn); double get_pressure(t_moldyn *moldyn); @@ -445,7 +481,11 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist); 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); +#else int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell); +#endif int link_cell_shutdown(t_moldyn *moldyn); typedef int (*set_hook)(void *,void *); @@ -466,6 +506,25 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a); int moldyn_bc_check(t_moldyn *moldyn); +int moldyn_read_save_file(t_moldyn *moldyn,char *file); +int moldyn_free_save_file(t_moldyn *moldyn); +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 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_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); +int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, + void *data,u8 bc); +int bond_analyze(t_moldyn *moldyn,double *quality); + +int visual_init(t_moldyn *moldyn,char *filebase); +int visual_atoms(t_moldyn *moldyn); + #endif +