some checkins

[physik/posic.git] / moldyn.h

diff --git a/moldyn.h b/moldyn.h
index 538e0eb..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) */
@@ -290,6 +291,11 @@ 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
@@ -438,7 +444,8 @@ 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 +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));
 
@@ -515,6 +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);