X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.h;h=a1866a98ac1ac0e4087f07344144d0e7763e69d1;hp=ee0a6dc87429495a99be906c7fbf8e409bb705aa;hb=8524173a28f2c22a539ef1b0910a1136d9cb254b;hpb=815b8841eb76564b2f90421d4eae180253453106

diff --git a/moldyn.h b/moldyn.h
index ee0a6dc..a1866a9 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) */
@@ -137,14 +138,22 @@ typedef struct s_moldyn {
 	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;
@@ -250,6 +259,43 @@ 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
@@ -396,14 +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,
-                   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);
@@ -452,6 +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));
 
@@ -471,6 +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);