some checkins

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index d065d43..a1866a9 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) */
@@ -258,17 +259,43 @@ typedef struct s_vb {
        int fd;
 } t_vb;
 
-typedef struct s_part_vals {
+typedef struct s_part_params {
+       u8 type;
        double r;
        t_3dvec p;
        t_3dvec d;
-} t_part_vals;
+} 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
@@ -415,18 +442,19 @@ 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,
+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,
-                   u8 p_type,t_part_vals *p_vals);
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+                   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,
-               u8 p_type,t_part_vals *p_vals);
+               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,
-             u8 p_type,t_part_vals *p_vals);
+             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,
-                 u8 p_type,t_part_vals *p_vals);
+                 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);
@@ -475,6 +503,7 @@ 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));
 
@@ -494,6 +523,7 @@ 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);