X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.h;h=0670f3d19239ada190d6c7d65fd99317392af295;hp=538e0eba8863bbb69f1071b72f07584e57a74dbb;hb=HEAD;hpb=dfb47bde6bf974d1b231048ec8bcda712404ccc1

diff --git a/moldyn.h b/moldyn.h
index 538e0eb..0670f3d 100644
--- 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);