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 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 {
int nx,ny,nz; /* amount of cells in x, y and z direction */
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
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 */
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;
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 */
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
#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
#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
#define CUBIC 0x01
#define FCC 0x02
#define DIAMOND 0x04
+#define ZINCBLENDE 0x08
+#define NONE 0x80
+
+/*
+ * more includes
+ */
+
+//#include "pse.h"
/*
*
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);
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);
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
//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));
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);
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
projects / physik / posic.git / blobdiff