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 {
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 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 */
t_random random; /* random interface */
double debug; /* debugging stuff, ignore */
+
+ /* potential 2 body check function */
+ int (*check_2b_bond)(struct s_moldyn *moldyn,
+ t_atom *itom,t_atom *jtom,u8 bc);
} 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;
+
+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_HO 0x00
#define MOLDYN_POTENTIAL_LJ 0x01
#define MOLDYN_POTENTIAL_TM 0x02
+#define MOLDYN_POTENTIAL_AM 0x03
#define LOG_TOTAL_ENERGY 0x01
#define LOG_TOTAL_MOMENTUM 0x02
#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 */
#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 */
-
-#define TM_R_SI 2.7 /* A */
-#define TM_S_SI 3.0 /* A */
-#define TM_A_SI (1830.8*EV) /* NA */
-#define TM_B_SI (471.18*EV) /* NA */
-#define TM_LAMBDA_SI 2.4799 /* 1/A */
-#define TM_MU_SI 1.7322 /* 1/A */
-#define TM_BETA_SI 1.1000e-6
-#define TM_N_SI 0.78734
-#define TM_C_SI 1.0039e5
-#define TM_D_SI 16.217
-#define TM_H_SI -0.59825
-
-#define TM_R_C 1.8 /* A */
-#define TM_S_C 2.1 /* A */
-#define TM_A_C (1393.6*EV) /* NA */
-#define TM_B_C (346.7*EV) /* NA */
-#define TM_LAMBDA_C 3.4879 /* 1/A */
-#define TM_MU_C 2.2119 /* 1/A */
-#define TM_BETA_C 1.5724e-7
-#define TM_N_C 0.72751
-#define TM_C_C 3.8049e4
-#define TM_D_C 4.384
-#define TM_H_C -0.57058
-
-#define TM_CHI_SIC 0.9776
-
-#define TM_LC_SIC 4.32 /* A */
-
-#define ALBE_R_SI (2.82-0.14)
-#define ALBE_S_SI (2.82+0.14)
-#define ALBE_A_SI (3.24*EV/0.842)
-#define ALBE_B_SI (-1.842*3.24*EV/0.842)
-#define ALBE_R0_SI 2.232
-#define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842))
-#define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
-#define ALBE_GAMMA_SI 0.114354
-#define ALBE_C_SI 2.00494
-#define ALBE_D_SI 0.81472
-#define ALBE_H_SI 0.259
-
-#define ALBE_LC_SI 5.429
-
-#define ALBE_R_C (2.00-0.15)
-#define ALBE_S_C (2.00+0.15)
-#define ALBE_A_C (6.00*EV/1.167)
-#define ALBE_B_C (-2.167*6.00*EV/1.167)
-#define ALBE_R0_C 1.4276
-#define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
-#define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
-#define ALBE_GAMMA_C 0.11233
-#define ALBE_C_C 181.910
-#define ALBE_D_C 6.28433
-#define ALBE_H_C 0.5556
-
-#define ALBE_LC_C 3.566
-
-#define ALBE_R_SIC (2.40-0.20)
-#define ALBE_S_SIC (2.40+0.20)
-#define ALBE_A_SIC (4.36*EV/0.847)
-#define ALBE_B_SIC (-1.847*4.36*EV/0.847)
-#define ALBE_R0_SIC 1.79
-#define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
-#define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
-#define ALBE_GAMMA_SIC 0.011877
-#define ALBE_C_SIC 273987
-#define ALBE_D_SIC 180.314
-#define ALBE_H_SIC 0.68
-
-#define ALBE_LC_SIC 4.359
-
-
/*
* lattice types
*/
#define CUBIC 0x01
#define FCC 0x02
#define DIAMOND 0x04
+#define ZINCBLENDE 0x08
+#define NONE 0x80
+
+/*
+ * more includes
+ */
+
+//#include "pse.h"
/*
*
*
*/
-typedef int (*pf_func1b)(t_moldyn *,t_atom *);
-typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8);
-typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8);
-
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
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);
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
-int set_potential1b(t_moldyn *moldyn,pf_func1b func);
-int set_potential2b(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func);
-int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
-int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
-int set_potential_params(t_moldyn *moldyn,void *params);
+int set_potential(t_moldyn *moldyn,u8 type);
int set_avg_skip(t_moldyn *moldyn,int skip);
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 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 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_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_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