Merge branch 'leadoff'

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index 538e0eb..0670f3d 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -45,6 +45,7 @@ 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) */
@@ -112,15 +113,18 @@ 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;
 
@@ -290,6 +294,11 @@ typedef struct s_defect_params {
 #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
@@ -352,6 +361,7 @@ typedef struct s_defect_params {
 #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
@@ -438,7 +448,8 @@ int moldyn_log_shutdown(t_moldyn *moldyn);
 
 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_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);
@@ -496,6 +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));
 
@@ -515,6 +527,7 @@ 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);